Did you ever pull the codes and see what the computer was telling you? If it was setting codes, it would save you a lot of troubleshooting time, as well as money on random parts.
Typically when you have a random misfire on all cylinders its either a MAF, or a bad crank sensor. '02's don't seem to have many problems with light flywheels and crank pulleys (mine has both and has never given me trouble) becaues their computers were simply not fast enough to process if there was a problem like that.
So, my guess would be crank sensor or MAF, based on what you say. But pull the codes and find out for sure. If you don't have a scanner, stop by your local autozone, they do it for free.