2004 Pontiac GTO Engine Idle

This is a 350/350 LS1 engine. I've owned the car since June 09. About 2months ago while the motor was warmed up, the idle began to spike upward about 250-300 rpm above the "norm" both in gear and in Park.
The "norm" has been 500 rpm in gear but under the above conditions it's running about 700-750.
This is throwing off the shift "pattern" whereas it's taken longer between shifts 1st to 2nd, 2nd to 3rd, and soon on. Oddly enough when the engine is cold the idle is back to normal and the transmission is ok. I've experienced situations where the engine is hot and running too fast, I shut it off, let it sit for a minute, restart it and it's fine temporarily until it spikes up again.
Now comes the frustrating part. Took it to my mechanic whom I trust and he diagnosed the problem as a TPS throttle position sensor. Took it home no change. After weeks of fooling around a GM factory rep came to his shop. He said the problem was the Powertrain Command Module and replaced it to the tune of $650. It seemed to be better at first but now not so. I know now I should have taken it to a dealer. Any suggestions? I love the car but now its not fun to drive anymore. Help!