Problem solved!
After drying everything out and making sure I had spark at all four cylinders, the bike would still cut out after a few minutes of riding. First cylinder 2 would stop firing, and the bike would run on 3 cylinders, but relatively smoothly. Then after 30 seconds or so, it would start having a fit and sputtering and wanting to die. It was bad.
I pulled the #2 plug cap to measure its resistance. It is only a couple months old, but I remembered that I didn't put the rubber seal on the wire side when I installed that cap. The wire is very short, and the insulation wouldn't allow the seal to slip on- if that makes any sense. Anyway, that cap measured ~11k ohms!
I replaced the cap with an old 5k that is still in the 5k ballpark, trimmed the insulation, and installed the rubber seal. So far, so good. I think the missing seal let water into the cap/wire connection and somehow shorted/burnt the cap. I can only assume that the bad cap was causing the intermittent firing issues.
As of now, the bike runs like it used to- pretty great. But I'm going to take all of your advice and install the fender as soon as it shows up, and I'll probably seal the ignition cover just to be safe.
Thanks guys!
TF
