Do you have access to a scanner? At this point I have a feeling it could be a few things, but you won't be able to figure it out without a scanner.

For example: I was having an issue where under different engine loads, the engine would stutter and fall all over itself. Scanning the car revealed the the MAF sensor was intermintently dropping off to zero and freaking the pcm out. Replaced sensor and the car's been good ever since.

So, instead of guessing for a predictable but intermintent problem... I'd get a scanner on there and see if any of the sensors are acting weird.