Engine starvation or what feels like engine starvation

I have a 1997 Mazda Protege DX with a manual transmission. It has been a fairly trouble-free car. It currently has a little over 172,000 miles on it. In 2000 just 2000 miles after it came out of warranty, the engine siezed. Mazda replaced the engine at half the cost. That has been the only major repair I’ve had to do with the car. However, late last year (2009), as the car was up for inspection, I noticed the car appeared to be missing and sure enough this was confirmed by the computer at the testing station, which found the 4th cylinder misfiring. The repair shop fixed that and tuned up the car and it drove like it had never driven ever. Beautiful acceleration, reasonably good response, etc. But that lasted only a couple of months and the symptoms I’d had earlier came back. The engine felt like it was missing and would wimp out exactly when I wanted the extra power, like trying to merge into traffic or pullout from behind a stopped car, etc. This time (as the colder weather had started to set in), I noticed that the problem cropped up only after the engine had warmed up. My mechanic looked at it and said it wasn’t misfiring. He identified (or so he thought) the problem as a faulty fuel pump after spending quite some time troubleshooting the issue. We replaced the pump and the car ran well for a couple of days. After than I began to sense the problem faintly once in a while, but not to the degree as to be troublesome. But over the past couple of months, I can feel it progressing to the same levels as I’d had earlier. What I also notice now is that generally, over speeds of 20 mph, when I experience the starvation sensation (or what I think is starvation), if I shift down a gear, the problem seems to go away. This of course is not possible when starting off from a standing stop.

Does anyone have any ideas what might be the problem with the car? I think my mechanic has run out of ideas.

When was the fuel filter last replaced?
If you don’t know when it was replaced, then it is time to do it.

When the fuel pump was replaced, was the tank thoroughly cleaned, ensuring no water or foreign matter remained?