Help 2001 tundra motor swap gone wrong!!!

Your Haynes Manual refers to the TPS(throttle position sensor) needing adjustment, which is correct. Taking the throttle body off does not require any adjustments on reinstalling.
If you wish to calibrate the TPS, the pics below might help unless Haynes Manual explains it well enough. You are aware you'll need an OBDII capable scan tool to adjust the final throttle valve opening percentage.

 

I have a snap on solus edge 18.4

 

Thank you for that info. You wouldn't happen to have a diagram for the engine wiring harness? I'm gonna replace the harness that goes to coils injectors throttlebody and couple sensors. Greatly appreciate it. Anything helps I've been dealing with this for over a year. Overwhelming. And my brother just wrecked my spare car so I'm really pissed

 

Holy Moly that’s a sweet looking scanner, makes my Techstream look like ekasketch !

You can download 2001 Electrical Wiring Diagram from below link courtesy of @RainMan_PNW

Ultimate Wiring Diagrams Collection | Toyota Tundra Forum (tundras.com)

If it's just TPS or APS, the below may work ?

 

Yea it's awesome. I gotta say this info is priceless thank you sooo much. You don't understand how much I appreciate this. I've been looking and can't get nothing. Thanks again. This is great

 

Holy shit I feel like I just struck gold. Right on man!!!!

 

Did you ever get this figured out? I have an 01 Tundra I had a motor swap done on and it’s doing the exact same thing and I cannot figure out what it is.