I need HELP !

I bought my 95 4runner v6 4x4 with automatic for $500 from a lady who paid $6000 for it . Her husband drove it home and parked it . The next day he had a stroke. It's been sitting for almost 11 years. The runner looks new.
The truck sat with a full tank of gas. I couldn't get a response from the fuel pump. Dropped the tank. The fuel had turned to a tar like substance. I cleaned it out and replaced the pump and filter. Flushed the lines. Replaced the injectors with 4hole upgrades. Hit the key after purging and she purrs like a kitten.
Put her in drive and she won't upshift from 1st. I can put her in 4H or 4L and she responds fine. So I dropped the front transmission pan ( 340H has 2 pans) pulled the solenoids and air checked with power and they work fine. I dropped the filter and pulled the bi-pass tubes and blew air on the ports to air check the clutch pack drums. The clutch Pistons and working and holding air passing the air check. The fluid was beautiful red and smelled and tasted yummy.
I started digging and had read that the input speed sensor if not working correctly will prevent shifting. I tried pulling code via OBD PORT WITH A PAPER CLIP. NOTHING. Ibecame suspicious of this and unplugged the throttle position sensor and re checked for codes. Nothing. So I start thinking the ECU isn't working. Yes she's working. My injectors are getting a pulse signal and are working. I replugged the throttle position sensor and retested for code. Now my CEL AND OD lights in the dash are both blinking rapidly and she won't start but will crank.
I'm pulling my hair out and hate to think of this beautiful 4runner becoming the center piece of a CAR-B-QUE ! PLEASE HELP BEFORE I FACE OFF WITH THIS RUNNER !

 

Man, you checked things that are way out of my league! Sorry, I can't help. But keep at it - and post pics! Good luck...

 

Thanks Catus. I just hate her sitting there. If and when we score another stimulus check I'm thinking of a manual transmission. Solve a bucket of issues.

 

Kaster,
The FSM is a god-send for troubleshooting. Mine already has a 5 speed manual in it so I am also not going to be much help. There are some pins on the ECM that are auto trans specific that the 5 speed does not use. That is about all I can add. Good luck with finding the culprit to your no go condition.
ATGP

 

Thank you.