Hey guys, registered just to post this because i think i have the answer as to why your car decided to work.
I had this same problem with exactly the same symptoms after replacing the water pump and all that jazz. And after trying everything i could think like replacing the distributor caps and rotors I took the distributor rotors off one last time and looked at the back. The little notch that is suppose to only fit one way when its bolted down was squished. Turns out in this image (step 12 of the excellent water pump guide) http://www.lexls.com/images/timingbelt/timingbelt18.jpg the rotors are facing the wrong way when the crankshaft is TDC, which it is in the image. Thats why the engine tryed and tryed to start but the firing order was odd. So Im guessing that when you put it back together that last time you put the rotors on correctly and bam, purrs like a kitten.
*edit* JPI got it on the last page, but yeah. Its so easy to put the rotors on wrong, I think it should be stated in the tutorial that the contact on the left rotor should be pointing at #1 on the distributor cap
