what year and what engine do you have? The computer controls the idle, so if you physically adjust the idle stop on the throttle body then it will alter the TPS sensor voltage at the idle position. Sometimes that can cause problems.
The Idle Air Control valve is what controls the amount of air allowed into the engine for idle speed. If you have a large vacuum leak it'll cause the engine to rev up and then possibly surge or even stall. If you check for intake/vacuum leaks and don't find any, then try changing the IAC valve.
Also, always remember to clean your MAF sensor, they always cause wierd problems when they're covered in oil etc. from K&N filters (if you have one).