Good point on the "coil ends" or whatever you call the rubber boots. I saw my name in the post someplace and like you, it just started missing one day. I replaced the all the rubber boots at the time I replaced the coil. To be truthful, I suspected the coil I replaced was good and the rubber boots were to blame but since it ran great, I was not going back in to see which cured the problem. My boots were not helped by a small oil leak that got oil in the holes where the plugs are at. I think this coil end or boot has the radio noise suppression resistor in it and that might have been the problem. I suspect I now have a good running car now with a good extra coil.
As a side note, I just took the car in for emissions testing (2-3 months after the problem) and the hydrocarbons were 6 ppm (max allowed is 220 ppm) and CO was 0.00% (max allowed of .8% I think). Must be running pretty clean!