I had been running into apparently intermittent ignition-related problems pretty much for as long as I've had my PAMCO (both mechanical and E-Advance), which I am pretty sure are not actually real ignition problems after all.
I would get this occasional hiccup where the bike would fall flat around 5k RPM. I made all the usual checks per Pete's suggestions, and everything was fine, or at least inconclusive; no real problem was to be found. I found the simple problem later, through a complicated procedure: a barely-loose connection at my main switch. Wiring in a temporary meter at various positions showed that the loose connection was providing enough resistance to "fool" the voltage regulator into treating the battery as fully-charged, and pulling back the charge voltage (a fully-charged battery shows more resistance than an empty one, I believe). The bike would run fine around town, but any significant blast would quickly drain the tiny battery down to the point where the PAMCO was gasping for current, while the voltage regulator simply wasn't wasn't sensing the correct battery resistance, and subsequently not supplying the required charge. A triple-check of all the battery connectors and a few extra toothed lockwashers solved the problem... and nothing in the ignition wiring itself was even touched.
A couple months later, I installed a new tach/speedo. Not too long afterwards (the correlation is obvious now, but was baffling at the time), a similar intermittent sputter started showing up. I could hear it, feel it, and most importantly see it on the tach; when the engine momentarily sputtered at 4k+ rpm, the tach needle would drop or bounce. Since the tach pickup was directly from the coil, I again assumed it was an ignition gremlin. I double-checked and/or replaced a handful of ignition connectors, checked the battery connectors, switches, etc., and nothing. The bike would test A-1 per Pete's recommended tests, but the intermittent sputtering continued.
Another month of this went by, until a fluke occurance revealed another piece of information... I don't ride at night much, but one evening pulling into my drive I felt/heard/saw the sputter, and also noticed that the speedo backlight was sputtering at the same time. Not the running lights or headlight, just the tach/speedo dial light itself.
The next day I double-checked all my gauge connections. Nothing seemed loose to me, but I went ahead and replaced a few remaining quick-disconnect fittings with soldered splices. I haven't had an unexplained intermittent "ignition problem" since. I haven't puzzled this one out too much, but I'm guessing that the intermittent connection to the tach was causing some sort of spike or feedback that disrupted power just enough to give the ignition a little fit from time to time (totally technical terminology, eh?)
Pete's PAMCO, with or without E-Advance is a fine, quality, and inexpensive product for the excellent results it typically provides. Follow Pete's troubleshooting guides to the letter, carefully wire things up, and expect excellence. However, I'm writing all this as a caution to those of us who may have failed to really properly 120% check their wiring for loose connections, faults, and poor grounds, and then blame the PAMCO.
I'm an electrician working as a professional marine systems installer, and I spend entirely too much time soldering wires in lousy spaces, troubleshooting weird fluky problems on boats. I'm confident in my skills and well-practiced, but I still screw things up from time to time. It took me three problem/solution cycles to fix my "ignition malfunctions", none of which seem to have been actual ignition issues. I'm not directing this to anyone in particular, but be advised that "double-check your wiring and connections" isn't something to skim over; it's fundamentally important.