Thanks TT,
First off, the timing light is made for cars, but I think it's working fine as it flashes normally on cylinders 1&4, then erratically on 2&3.
Second, my tuneup started with a valve adjust, filter clean (UNI foam filter in stock airbox), cam chain adjust, plug gap, and finally timing. Stupidly, I did a carb sync before timing because I had the carbs off for cleaning and bench synced them again, but I figured I could re-sync after the timing was complete.
I have seen posts indicating that the coils themselves rarely fail. My problem may only be with the plug wires and ends. But, even if the ends are bad, wouldn't the coil still fire normally? Or do the wires have to be part of a complete circuit, with ends and plugs all hooked up?
I don't know about the boot resistance, I'll have to check it. What should it be?
Thanks for the help. Unfortunately I am away from the bike until the weekend, so I'll recheck everything then.