1SIKAP1

I had the same issue and it turned out to be the ecu, i tried everything, and i finally swapped myy 00 ecu with a 02-03 and all problems went away, the one thing that gave me the clue was when i bought a vafc2,when i was playing with the fuel and other setting the missfire went away, but slowly came back, due to the ecu learning and putting the stock 00 ecu tune back to where it wanted it to be, i would reset my ecu and the misfire went away. Thats when i decided to swap the ecu and finally got my engine to run normal.