OK, I don't know how far things have diverted from the original question at this point, but I've been having a very similar issue:
1) motor "cuts out" a lot, meaning it acts as if it suddenly loses spark or fuel, just for a second, then regains and runs again. Its especially bad several minutes after its been running and before it warms up completely. Sometimes it stalls out completely, and have to restart. Often while its driving during this period, it behaves similar to how if you're running out of gas (and we've all been there, admit it) and using the last few drops of fuel and you get that "surging" effect. After it warms up completely, it pretty much goes away, except for occasionally stalling out, especially when I'm at a light right after it turns green (of course).
2) I had it hooked up to a diagnostic and it showed no issues with spark or fuel. The supposed explanation is that there is a lot of carbon buildup in the motor and it will just have to slowly burn out. I've been filling up with high test, plus a couple containers of octane boost, plus a dose of Seafoam, each time, and the problem has been marginally getting better.
Hope this helps, or at least rings a bell with somebody.