Not sure about this one ,,, just recalling from memory

After transmission re-build the ecu needs to be reflashed.

Knock sensors try to adjust timing (retard- advance) till they can not compensate and the CEL comes on and later o/d i locked out

 

I've only went on short 2-3 mile trips should I try and take it on a 10+ mile to see if it changes? I unplugged thw iac and it wouldn't idle till it was warm and then idled fine

 

Not necessarily re-flashed, but just reset. You can do so using the Toyota Techstream that can be found for cheap on the Internet.

However, I don't think that's the case here; if the transmission was shifting fine before starting the repairs. Was it OP? I don't think the OP has mentioned if it was running fine before.

 

I FOUND THE PROBLEM!!!!!! I didn't take it off but there was a ground wire that must of been on the side but was suppose to be on the back it was tight but would have stretched to the grounds on the side but found the hole it was suppose to in and hooked it up. Runs like new!! THANK YOU FOR THE HELP!!!!!

 

Glad you found the problem! Where was the ground supposed to connect on the manifold? Passenger side or back center?

 

I know it wasn't in the back of the mantifold but that's where it was sitting but there was enough wire to pull it to the side, I can tell it was taken apart before (black gasket blue spark plug rings and silver rtv) and I bet the person pulled it to the side, and when I took it off went back to its natural location and I didn't notice

 

Folks 'any' ground is not the right solution.

There are current loops inside the body ground, almost like water currents in ocean.

There is engineering involved in finding the right spot for ground for each circuit.

Salim