Well, the cause of this problem is (sorta) a mystery to me. I went on a pretty long ride on Sunday (the "Tour Da Bay" ride) and had no issues. I did, however, put a Monster in the trunk and forgot about it. Monday morning I went off to work (about 15 miles) and she started with no issues. On my return home I stopped to get petrol and when I went to turn the bike back on it merely clicked. At this point I found the Monster can I had forgotten in the trunk with a hole in it. I then tried to jump the bike and the results were as follows: clicking, clicking, ten minute wait, no clicking, it started and then I shut it off, ten minute wait, clicking, started and then it died after a few moments. By the final start I noticed the headlight was very dim which meant it was probably only running off the battery.
I got the bike towed home and today I charged the battery then went through Makis' charging system check. Across the battery I got 12.6V at idle and 12.2V at 4K RPM. I then went through the manual's system check and found that all the readings were out of spec for the stator. The rectifier seemed to check out ok and I went ahead and checked all the fuses as well.
My question is; what could have caused the stator to go bad (aside from sugary goodness spraying around in the trunk) and what else should I check out while I have her half-nekkid? I also decided to take off the L side radiator as it had recently developed a leak. Hopefully I can have it repaired and find a stator for a decent price. I see Ben has one so I'll give him a call. I want to thank everyone who has made this site the wealth of information (and jackass-ery) that it is today.