The OFFICIAL manual swap thread

1. I know both the 4spd and 5spd auto's in these 4runners are fantastic transmissions. I know auto's are better offroad and for daily driving. I don't care, I like driving manual.
2. This is not a 100% step-by-step guide and will require your own part number and compatibility research. You will need your own wiring diagrams and some mechanical ability.
3. This only applies to 1GR V6 4runners. I'm sure you can do this swap with a 2UZ but it would likely be more difficult.
4. There's way more then one way to do most of the tasks I'll cover - think outside the box.
5. It's pretty easy. Time consuming with some custom work required here and there, but overall it's not a difficult swap.


Candidate - 2004 4runner SR5. 4wd, V6 1GR, 4spd A340 auto, 147k miles.


Let's get started -

My trans donor
- 2013 FJ crusier RA61F 6spd with 150k miles. Any RA61F from a 07-14 FJ will work, but the 11+ RA61F technically has a superseded part number despite being the same externally and having the same gear ratios.

Other trans donors you can use
-RA60F from a 05-15 Tacoma. Same a RA61F, expect 6th gear ratio is 0.849 vs the RA61F with 0.799.
-RA62F from a 16+ Tacoma. Would need modifications for the tcase described here and possibly other things for the swap that I don't know about: https://www.tacomaworld.com/threads/fj-case-in-a-3rd-gen-tacoma.571689/

Clutch
-New Luk flywheel and Aisin clutch kit. Ran the Clutch Masters internal slave conversion to simplify the clutch hydraulics and avoid the RA6X Achilles heal input shaft issues.
-Conventional hydro setup can be used, but I'd suggest at least the URD input shaft repair sleeve.
-Make sure you buy the clutch kit from whatever year/model trans you buy - even though they all bolt to the 1GR, they have different part numbers and I don't know why.

My Tcase #1
-Manual tcase from a 2023 4runner TRDOR. You can use any tcase from AUTO trans 07-14 FJ's or any tcase from 2010-2024 TRDOR 4runners. They are all the same from what I can tell.
My Tcase #2
-Any 05-15 Tacoma electronic tcase from a MANUAL. You will need the tcase input housing/shaft to swap onto your FJ/4runner case, as described here: https://www.tacomaworld.com/threads...s-for-fj-case-for-manual-transmission.714337/

Trans mount - You can use either the manual mount from a Tacoma (Possibly FJ?) or your original 4spd auto mount (Possibly 5spd auto too?). They are exactly the same - both bolt directly to the RA60/1F trans and directly to the original 4runner crossmember with zero modification. Big win

Exhaust - no modifications needed

Front Driveshaft - Needs to be shortened 2" in my application
Rear Driveshaft - Needs to be lengthened 2.25" in my application
I'm running custom Tom Wood's driveshafts, but I did use a 1.5" Trailgear driveshaft spacer for the rear temporarily to test drive the swap without issue.

Trans and both my tcases


Input shaft swap that's linked above


End result: part-time 4wd manual FJ Case with the RA6X manual input housing and shaft


A340 and electric shift tcase next to my RA61F and manual tcase. Note the length differences




Clutch Masters slave install


Trans bolted in and primary hole cut for both shifters.





ALRIGHT - Lets setup the clutch now.
Clutch pedal assembly from a 2007 Tacoma
I went ahead and did the metal FJ clutch pedal and metal master cylinder swap into the Tacoma assembly, as instructed here:
https://www.tacomaworld.com/threads...al-for-a-metal-one-from-an-fj-cruiser.814720/



Narrow manual trans brake pedal swapped from a manual 2009 FJ, right into original 4runner brake pedal bracket.



Remove the ebrake pedal - that's gotta go. I removed the complete mechanical ebrake including everything behind the rotors and the cables and converted my parking brake to dual line locks. See reply #25 for my write up on the hydro line locks, but before that you'll see me and other members discuss other ebrake options too like using a 3rd gen Tacoma console. Relocate your ABS control unit while you're in there - I mounted it up against the left side behind the body control unit.

Once you get in there you'll see this "hump" of metal riveted to the firewall next to the brake pedal. Drill the rivets off and remove it.



Cut away some of the insulation and bam, your clutch bracket will fit nice and flush on the firewall, You can even use these existing studs/stud locations with minor modifications.



This is where you clutch lines will go, mark and drill your holes.



Tacoma clutch res mounted, short hardline section made up and connected to the stainless braided line from the Clutch Masters slave running up the firewall.



So you trans, clutch, and tcase are ready.

Let's dig into the console.
I used a 2nd gen Tacoma console. I wanted an console armrest, functional cupholders, and a good aesthetic. Fair warning, I spent more time making this console setup work then anything else in the entire project. Massive cutting is required to fit the front of the Tacoma console against the angled asymmetrical 4runner dash.

I cut the top layer wider then the bottom cut of the trans tunnel so I have a flat section to mount shifter insulation.

Don't forget to cap the HVAC duct that is running to the rear


The space where the old 4wd knob was is 60mm after you grind down the inner lip. They do make 60mm gauges, so this would be the perfect spot for one. I opted for a 60mm blank plug, and maybe down the road I'll do a supercharger and swap this out for a boost gauge.


Note: All 3 OEM Tacoma console mounts retrofitted to the 4runner body. Holes for auto shift cable and ebrake cables plated over/sealed. Shifter boot insulation from a manual FJ cruiser installed. Yaw sensor control unit (required for functioning ABS) harness extended and the unit relocated. Connector installed from cig lighter wires to custom accessories harness on the Tacoma console (USB ports, streamlight charger, etc)
See reply #16 for my attempt at making a shifter boot setup
Not pictured - Added foam insulation under the console to cut down on noise.

Trans shifter cut, bent slightly to the driver and rewelded
Tcase shifter completely custom made to be skinny enough to clean 5th and 6th gear in 2hi/4hi, and not contact the side of the console when shifting in 4L.








Electronics! Everyone's fav -

I deleted my front axle disconnect (ADD or CAD) as described here: https://www.tacomaworld.com/threads/how-to-deleting-add-system.427258/


I wired the Tcase 4wd indicators directly to the indicators on the cluster. Made a little custom harness then used no-longer-used wires from the old transfer case actuator to the now completely removed 4wd module.


The plugs for the 4wd module which is fully removed. You can see where I used the original 4wd actuator wires as a vessel for the signal lines - jump them directly across to the indicator wires heading to the cluster.



***
- The vehicle WILL NOT start if it does not think it's in park. You will need to splice some wires together to do that - you can do it either on the side of the trans where the neutral safety switch was, or inside the 4runner right at the DME.
At the neutral safety switch connector on the side of the trans you will need to splice pin #9 (pink) with pin #6 (black/yellow).
As I'll explain below, I did this splice directly at the DME. To do this you would need to splice together ECM connector E4 pin #16 (pink), connector E5 pin #9 (pink) over to connector E4 pin #17 (black/yellow),
This will change between years!! Check your own wiring diagrams. The key is to have to the starting system wires always jumped so the DME thinks it's in park.
- There is another set of "park" wires at the neutral safety switch - pin #1 green/black on my rig. This illuminates the P on the cluster - This does not need to be spliced for the vehicle to start and is simply for the cluster.

- If you want to have a clutch safety switch for starting, wire the factory clutch start safety switch to the splice you made (This is why it's ideal to do the splice at the DME). Have the 2x pink wires splice together, run to the clutch switch, then have the return leg from the switch run to the black/yellow wire.

- Splice your manual trans reverse light switch from the power wire (pin #3 yellow black) to the reverse wire (pin #2 red/yellow) at the neutral safety switch.
***

- I have not at this time figured out how to make cruise control work, but I will update if I do.
- UPDATE - Cruise control is now working. You may run into different road blocks for the 05+ ECM's, but the 03/04 ECM's are dumb as hell. You will need to splice 12v power to pin #10 (green/yellow) on the E7 ECM connector. This circuit is labeled "D" as it lets the ECM know you're in drive. I got the 12v from ECM connector E8 pin #9 (black/orange) which is a 10amp fused power circuit when the key is on "run".
- Here's the kicker, You can wire it so the "park" circuit wires are jumped and the "D" wires are jumped separately at the same time. No fancy relay work needed - the ECM will see that's in park and drive at the same time, you will continue to have a fault for the park position switch stored, but cruise will activate.

- To have depressing the clutch kill cruise control as it should, you can wire the factory clutch cancel switch to the "D" circuit you spliced. This switch is a NC or normally closed switch, and therefore when you depress the clutch it will open the contacts and the ECM will think you shifted out of drive and cancel cruise.


THE CLUSTER.

- If you have a 05+ there is a good chance Overland Tailor Tuning can flash out your auto trans DTC's - I emailed them and they actually confirmed they could do this on the 05-09 ECM's. They weren't sure of any side affects, but it would be a good place to start.

- If you have a 03/04 your ECM trans parameters are not reflashable. You will have a CEL for the missing auto trans - faults include 2x trans range sensor circuits, all 4x shift solenoids, and trans fluid temp. You could attempt to simulate these manually - A resistor for the trans temp, 4x relays hooked up to nothing to simulate the shift solenoids, and possibly some clever switch wiring could simulate the park position switch.
I have no emissions, and could not be bothered as none of these faults effect drivability. I also wanted to get ride of the VSC lights on from removing the ADD and 4wd control unit.

If the last part above is your case too, pop your cluster apart.


Don't wanna look at the light? Cover the LED with some JBweld putty.
Also, not pictured, but remove the light transferring plastic over the PRNDL so they wont be receive the amber back lighting everything else does. Won't black them out completely, but it's a lot less noticeable.


Perfect!


Remember the splice for the reverse light switch? Little bonus - when you shift into reverse your cluster will remind you!


4hi


Tcase neutral - yes I took the time to splice it into the "N" on the cluster too


4Low


Running (Well the door is open, but that goes out of course)




Cool, now go row some gears.

 

epic

 

Fantastic write up , great dedication to detail and doing everything to ensure a professional and user friendly finished product . The Tacoma center console really finishes off the interior nicely .

 

Impressive work and nice first post! You're not going to ask what size tires will rub?

 

Hey OP , how about some pics of the truck when you get some free time, what other mods do you have planned ? I heard a rumor there could be suspension, wheel and tire and bumper mods in the near future . Post em up !

 

Excellent write up Jakobies1086. You have a very OEM+ look, especially with the Tacoma center console.

In researching doing a manual swap, I can't loose the ebrake as I do enough off-roading that it's a must keep. Though I had not considered a line lock. I haven't eliminated the option but will be doing the manual tcase here this summer.

 

Awesome work!

 

Thanks for the feedback guys. Truck is a blast to drive, feels like a 2nd gen Tacoma.

With some firewall and Ebrake bracket modification I think you could keep the Ebrake pedal, just move it closer to the firewall. I opted against that as it seemed like unnecessarily big undertaking in an awkward spot to work.
Another option I heavily considered was using a 3rd gen manual Tacoma console - the 4runner Ebrake cables T-off on top of the trans tunnel and it would be easy to connect it to the handbrake style lever like found on the 3rd gen console. I opted against this because I couldn’t find a cost effective 3rd gen console and I was worried it would be substantially more difficult too graft into the 4runner due to the difference in vehicle age.
An honorable mention is the FJ cruiser manual console, which is wider with provisions for both shifters and has a handbrake lever. The downside to that option is it has no armrest console box, because the FJ seats have armrests on them. You could always take this route and try and fit some FJ seats too.

I ran a line lock to the rear as a parking brake in my old 93 pickup SAS’d crawler, and it was phenomenal. I used a covered single pole switch, a relay, and had it wired to illuminate the parking brake light on the cluster. It’s extremely easy to wire and to plumb, everything is under the hood except the two switch wires running into the cab. It would always hold on extremely steep rock faces so I could get out and spot my line choice, as if I was sitting in the truck with my foot on the brake. I wouldn’t leave it set with the truck off as it will draw on the battery and would release in a low-voltage scenario, but with any manual vehicle I have I always just leave it in 1st with the parking brake off.

In the 4runner I have the same electrical setup ready to go, but I haven’t settled on the line lock simply because it has a 4 channel brake system so you’d need two locks to hold both rear wheels. Also, it’s kinda tight up there plumbing-wise, so it might be tedious to fit two. I might just a settle with one holding the left front wheel as that would be adequate for 95% of situations I use a parking brake (running into a store with the truck running, taking a piss on the side of the highway, moving cars around my driveway, etc) but I wouldn’t trust it off-road nearly enough without two wheels locked, so I’m also considering doing both fronts as that’s easier to plumb then both rears in the engine compartment.

 

You probably have already seen his post: https://www.4runners.com/threads/4th-gen-manual-swap-thread.16676/

It wasn't shown in Diego's post, but in another Reddit Post (https://www.reddit.com/r/4Runner/comments/k7nl8c/finished_the_manual_swap_where_my_4th_gen_guys_at/), but it looks like he figured out a way to mount an ebrake handle by the shifter.



I guess as they say, you are only limited by your imagination (and the size of your bank account).

 

Yeah I’ve seen his swap - that lever sticking way up infront of the console appears to be a hydro Ebrake handle which do not lock on and are for drifting. I’m not knocking it, everything depends on what your standards are and what you want out of the rig - his console has no cup holders, exposed rough cuts, and the poor booting around the shifters is gonna transfer a ton of noise and harmonics into the cabin.

 

Yeah, I should have picked up on that. Not building my 4Runner as a drifter or for rally cross. And I agree on the console. I would prefer a more finished look.

 

Definitely more then one way to get it done thou - if I wan’t so keen on ditching the drum parking brake for a line lock I’d say the 3rd gen console is the way to go. I really think connecting the hand brake in one would be easy work and the remainder of the console swap is similar to the 2nd gen

 

awesome write up. looks super clean

 

Absolutely incredible!

 

Awesome work, btw I have the vertical console surround that came out of a 2WD 4Runner without the 4WD selector switch in my shed if you want it. Just pay for shipping. Also it is painted black. I dyed my interior black because I swapped my seats.

 

Thanks! It never even crossed my mind that they made these in 2wd and you can get that trim without the cutout for the 4wd knob; as a lifetime resident of the north east salt belt I've never even seen a 2wd 4th gen for sale locally or in person! I do appreciate the offer but I'll keep mine - I am planning on installing a gauge in that spot, specifically thinking the Banks iDash along with a 60mm-52mm adapter

So I visited a upholstery shop to tackle the shifter boots, and they told me to pound sand. I decided at the expense of it looking good I would tackle it myself instead.
The transmission shifter boot is a OEM Toyota boot. I cut a slot in the side for the Tcase shifter. The Tcase shifter boot I bought

$8 Gear Shift Boot Cover,Car Gear Shift Knob Gaiter Boot PU Leather Dustproof Cover Replacement for Toyota Corolla

here, on Amazon. I can't sew and I couldn't be bothered to try to learn, so I bought a leather hole puncher from Home Depot and stitched with small black zip ties. It looks decent

 

Daaaaaang! Looks stellar! I could only imagine the driving of it!!

 

I drove a manual Saturn for 6 years and a 5-speed Xterra for 11 more. Really enjoyed it most of the time, though stop and go traffic was tedious.

I read this thread and heard Darth Vader in my head. "Impressive. Most impressive!"

 

That's awesome! How's the ergonomics with the shifter and pedal? Pedal throw seem right? The reach to the shifter feel too close or too far?

 

It's remarkably good. I'd say its within 5% identical driving ergonomics to a 2nd gen Tacoma. The clutch throw, level, and its placement with the manual FJ brake pedal is identical. Seat to armrest/shifter placement is perfect for me - its been a while since I drove a 2nd gen 6spd but I recall it being extremely similar. The only significant difference is the 1/2" or so I bent the shifter towards the driver to clear the Tcase means in reverse (and somewhat 1st and 2nd) the shifter is a bit closer to my knee (I'm 6' 2" and I manspread in cars) but its not uncomfortable. Shifter reach and the way my arm sits on the armrest is perfect.

I will say I am planning on adding a proper plastic clutch stop. Currently it maxes out when it hits the floor, which is plenty disengaged and isn't a problem but I am going to install one for a more firm endstop.

I'm currently in the process of installing the line locks as a parking brake and I'll update when I'm done. I'm also going to install a clutch start safety switch - I already started it in gear once cause I'm an idiot, and the whole 4runner/Tundra crank-till-starts when you just bump the key means accidently doing that in gear is super sketchy.

 

The manual transfer case swap and add delete are on my todo list (usual problems with switching in and out of 4x4 with the electronics). I dig the idea of a manual trans, but I don't know that I could justify it. How much do you think you have into it all?

I've always disliked the foot e-brake. My second gen Tacoma had the same. The third gens had a hand brake. Any reason you didn't go that route? Third gen Tacoma console with hand e-brake? Why a line lock?

 

Man I'm glad you're alright, but I laughed something fierce as you were explaining the crank until start function and it being a manual now...Bravo, sir!

 

I don’t have a total cost added up tbh, but it wasn’t cheap. The trans and tcases alone cost me $2k, $1k in driveshafts, couple hundred in console parts, plus another $1k in clutch parts. That doesn’t include the add delete, clutch pedal stuff, etc. as a rough estimate I’d say I’m about $5-6k into the swap.

I ran a line lock before as a parking brake in a rock crawler and I really liked it. I also liked the simplicity of no additional cables, no fancy calipers, no drum assemblies inside the rotors, etc.
I ran the 2nd gen console over the 3rd gen because of cost (saved me about $500) and because I figured it would fit easier/better as the 2nd gen Tacoma platform is a lot closer to the 4th gen 4runner then the 3rd gen Tacoma.

That being said, like I mentioned earlier in the thread I think the 3rd gen Tacoma console swap with the hand Ebrake adapted would be similar in effort and function. If I ever do it again, I’ll be inclined to give that route a try.

 

Haha yeah I love the feature normally, but when the stater is now relentless pulling you forward down the driveway till you can jam the clutch in… yikes
I have the connector and pins from Toyota for the clutch start switch, I’ll update this with the part numbers and everything once I get it all installed.

Also, I’m working at trying to find a solution to get cruise control working. Unfortunately the 04 DME trans is not tunable so I can’t get the auto trans inputs flashed out, and at least some of the faults are prohibiting cruise activating. I’m gonna start trying to narrow down which faults exactly are causing that, and then trying to find a work around.

 

So I got cruise control working which was a HUGE win for me, and a clutch safety start switch - it was actually pretty easy and I have updated my original post with that info

I also finished my line lock parking brake. Despite everyone's concerns, it works absolutely perfect. I went with two line locks under the hood, one for each rear wheel as these 4runners have 4 channel ABS and I didn't wanna splice them together. I would not leave this on overnight as it draws power and I'm not sure how long you could leave it on with the engine off before it kills the battery. I don't care about that at all, when it's off I just leave it in gear and no e-brake like I've been doing with all my manual vehicles for the last 15 years. When it's running you could leave this type of parking brake on all day, and it holds 10x stronger then any cable ebrake so I can safely get out of it running in neutral to spot a line choice, open my garage, grab takeout, whatever.

For wiring I just wired the two units together directly to the battery (well through a 10amp fuse first). The ground I ran into the cabin, through a safety-covered toggle switch, and to a chassis ground point. I also spliced in pre-switch the wire for the original parking brake switch, so when I throw the switch it turns on the parking brake light on the cluster just like its OEM. To activate it I just press the brake normally, flip the cover up and then flip the switch up then release the brake pedal. It holds with the hydraulic force of however hard you were pressing the pedal when you flipped the switch. So If you're on a super steep hill sitting there with your foot on the brake not moving and you flip the parking brake switch... you can hop out and the truck won't move a millimeter. Having two locks gives me some mechanical redundancy too if one were to fail. The way I have it plumbed I did not modify the OEM rear brake lines and could easily disconnect the lines I added, re-bend the OEM line by hand and reinstall directly back into the master, bypassing the line lock on the side of the trail in the event of a unlikely failure where it locked itself on.

 

Damn right incredible!!