That really sucks. The Dealer had better not stuck you with any costs. The TRD S/C is fully warrantied whether Dealer installed or not. At the minimum of 12 months/12K miles. Either way, if it is not on the motor, how can it have been the problem. Scion techs are actually Toyota techs whom have very little, if any, training on our cars at all.
Anyway, that is a different topic all together. Now for your current issue. What codes are you getting now? The TB is drive-by-wire. Did you check the accelerator pedal potentiometer? You are probably experiencing the following:
FAIL-SAFE
When any of these DTCs, as well as other DTCs relating to ETCS (Electronic Throttle Control System) malfunctions, are set, the ECM enters fail-safe mode. During fail-safe mode, the ECM cuts the current to the throttle actuator off, and the throttle valve is returned to a 6.5° throttle angle by the return spring. The ECM then adjusts the engine output by controlling the fuel injection (intermittent fuel-cut) and ignition timing, in accordance with the accelerator pedal opening angle, to allow the vehicle to continue at a
minimal speed. If the accelerator pedal is depressed firmly and gently, the vehicle can be driven slowly. Fail-safe mode continues until a pass condition is detected, and the ignition switch is then turned off.
I really need your codes to focus down on the problem. Does the engine idle normally or is it severely rough?
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How Fast Was I Going? 
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