This is a difficult problem to even explain, so please bear with me on this.
As I kept putting more performance mods on my car ('99 Alero V6), everyday drivability kept getting worse (no surprise there). In particular, the idle was not stable, especially on a hot start-up-- had to keep throttle open a bit till it got into gear. I was able to band-aid the problem by introducing a controlled vacuum leak just after the supercharger. A couple years ago, A friend reflashed a spare VCM with a copy of his stock 2001 Alero program. I put that in my '99, and got perfect drivability. But using the 2001 VCM has two glitches--the Charge warning light and chime come on because the alternator wiring is different in the '99. And I can't change the coolant fan settings in the '01 VCM, but I can with the '99.
Recently I added an intercooler and upped the boost, and the problem is more severe.
The worst symptom is, I'm at a stop, step on the gas, and you hear a little rush of air, and the engine stumbles or dies. The faster you hit the pedal, the quicker it dies. If I set the target idle to 800 rpm or more, I can drive the car, but it still has some hesitation and runs rough. I put the '01 VCM program back in, runs fine.
I have tried copying every engine and trans table from the '01 program to the '99 VCM with no luck. Would appreciate any help.