Just a bump for this. Earlier this week it rained pretty bad. This time the right side wouldn't fire at all and the left was pretty rough at higher rpm too. As the week progressed, something dried out and the left started firing fine pretty much throughout the rpm range, but the right side was still dead above 1200 rpms. At idle, the bike ran ok. Today I went out there and swapped the plug wires/boots from one side to the other. No change. Already swapped the coils. So the issue is up stream of the coils.
Again, at idle, the bike sounds somewhat OK, but as soon as I give it some fuel, it cuts out on the right. At that point, I went ahead and took her around the block to warm her up more, got up to 3rd gear and kind of putted along. Left firing fine, right missing every revolution or so until after 4 minutes, it started kicking in and eventually came back online and ran fine.
I guess I'll just start messing with the multimeter and work my way back from the coils, but this only happens when it rains or when there's a lot of dew, so tomorrow it will probably run fine. Like I mentioned before, maybe I'll hit it with the hose and see if a certain area affects it. Any ideas??