Help on next steps...Rough Idle Issues

Hi all. I have a 2001 4Runner with approx. 280,000 miles. Recently noticed a bit of a rough idle for several seconds in the mornings from cool and then idle would set and ran fine. I was too busy to check until one day, I put it in reverse and noticed a significant "putter" and rough throttle when accelerating. Checked under the hood and found that the air intake hose to the throttle body was dry rotted and cracked. I replaced it thinking it would fix the issue and while I had it down for repair, cleaned the MAF, checked air filter and cleaned the throttle body. Cranked and it still had the issue so I got new spark plugs thinking that may be the issue. This improved the issue but still a rough idle and around 45-50 mph, a rough acceleration and shudder feel from running lean. I pulled the throttle body off again and cleaned it again and this time sprayed all areas I could and noticed the PCV line had gunk in it so I replaced the valve and cleaned the line. I also checked for any noticeable holes in vacuum lines and don't see anything. Currently, without air conditioning, it seems to be trying to set itself to the right fuel\air mixture but still struggles at lower RPMs. When the air is on, it is worse running conditions....lots of sputter and almost a misfire feel but no backfire or any smoke from exhaust. What would you all suggest I look into next? Any advice is much appreciated and needed, thanks.

 

Couldn't hurt to pull sparkplugs,.. just one cracked plug and it will idle rough and miss. Check the simple stuff first.... oh wait i see that you checked those already,. lol my bad.
How bout fuel filter? could be fuel related

 

Thanks, yeah I did those. I was looking into parts just now and see that I could try the throttle position sensor....it may be fried

 

yeah,. time to bust out the multimeter. havent had a lot of experience with the 3.4 and its quirks,. hopefully the 3rd gen crowd will chime in