I have no idea what happened to it then. All I know is that both cables are very short and are not in good shape. I'll be re-wiring the bike this winter because the wiring is mostly pretty messed up.
I just installed the new R/R today, and rode it around only to find that I still have some issues.
First, I checked the voltage of the battery before starting, which was at 12.6V. Then I checked voltage at idle, which was jumping all over the place. I realized that it was because of the electrical noise of the bike, so I held the multimeter as far away as I could and measured again, and it was a steady 12.25V, and jumped up to 13.0V as soon a i gave it a little gas. I figured it was idling a little low (it was still warming up) which caused the low voltage reading. So I rode around and it was running great.
Then I noticed as I was coming home, I noticed the turn signal running lights were getting dim, so I turned the headlight off (I have a button rigged in the headlight circuit) and they got pretty bright but were flickering a bit. Then it started getting closer to dying as I was getting close to home, so I left the headlight off for the last few blocks. Checked running voltage with headlight off which was 12.2V, then battery voltage right after turning it off, which was 12.15V.
I have a couple different thoughts as to what may be wrong. I just installed a Dyna S, so that is using ~1 extra amp/12V over stock, plus I have a 45W headlight, so another 15W/1A over stock. I also have a smaller than stock battery, so maybe I am draining the battery really fast? Or maybe I am heating up the ignition switch because of too much current? Or is it possible that I fried my stator/rotor when I hooked the battery up like an idiot? Is there a way to inspect the charging system?