Don't worry 'bout me. Watchin' the race in every room! LOL

To the op, I would hope after all of this changing of pumps, etc that the mechanic was verifying that it was loosing fuel pressure when it would start to run funny. Something as simple as water in the tank can cause issues such as these.

If the pressure doesn't droop when you are having these problems, then I would say it isn't a problem with the pump.

If it happens after a certain length of driving, then I would lean more towards something in the ignition (ICM) heating up and fouling.

But again, I would think that your mechanic would have pin pointed it as a fuel issue.

If it were me, I would remove the hood and drive it for a day with a fuel pressure gauge installed, watching it. If at that point a fuel pressure issue is noted, I would dig into the inputs that control the fuel pump. Those include voltage supply to the relay, voltage at the pump, PCM trigger for the relay, etc.

HERE is a thread that had quite similar symptoms to yours... Turns out it was a problem with the wiring modifications that were necessary for the pump that was used. However, that thread covers everything that should be checked quite well.

Hope this helps!