Did you make sure that you set the TPS right? Is IDL and E2 are not making closed at Idle it will cause the idle to surge or even stall when the brakes are pressed (the ECM monitors the brake light switch as well).
Roger has some good information on his site on adjusting the TPS and checking the AFM.
http://www.4crawler.com/4x4/CheapTricks/TPS/index.shtmlhere are a couple FSM for the MkII and MkIII Supra. A lot of stuff like the AFM, TPS and general trouble shooting are the same. The codes won't be and the MkIII uses a IAC but the FSM trouble shooting list is great and valid for diagnostic.
http://www.cygnusx1.net/supra/techtips.html Between that and a Haynes or a Chilton's your set. The W58 used in the supra is nearly Identical to the W56 in the truck. Only big difference is the tail housing. I used that MkIII transmission section when I rebuilt my W56. It was spot on.
