It sounds like you have covered a lot of posibilities. There isn't much left in the ignition system that could explain it.
Some other things that can cause a mis include:
lean mixture (fuel pump, plugged filter, vacuum leak, dirty injectors)(some vacuum leaks can be tricky and even intermittant)(fuel quality has even come into play here, too much alcohol can play havoc if the system doesn't have enough mixture range to accomodate the leaner running fuel)
valve problems (weak springs, valve starting to burn, carbon shrouded valve, worn cam lobe)
cam timing issues
carbon build up in combustion chambers
ring flutter (usually only at high revs on a "loose" engine)
I have seen all of these things cause wierd engine misfires, and they were often hard to track down.
Have you tried driving it with a fuel pressure gauge installed while it is acting up?
Good luck with finding it.
