Thanks, that reminds me of something I forgot to mention in my original post.
There was one time a couple months ago that I went to go for a ride, and for some reason the bike didn't want to start. It was acting like it was flooded, and after trying unsuccessfully to start the bike I drained the battery. I pulled the seat off and removed the battery, and in doing so I noticed 2 green wires back by the rectifier that were melted, and I think I bumped one and broke it off. I took the battery home and charged it up, put it back in the bike, and it fired right up. I took a few short rides, and I assume the bike was not charging and just running off the battery because of the broken wire.
When I found some free time I cut out the melted wires and soldered in some new wire. When I was done I put a multi-meter on the battery and verified that it was being charged with the engine running. It appeared as if I fixed that issue.
That brings me to last night.
So, last night I went to my storage unit and looked over the wiring around the fuse box. I removed the right side fairing and looked over all the wiring there and I didn't see anything obvious. I made sure all connectors were snapped in and snug, and wiggled everything to make sure all wires were secure. I even started the bike and wiggled wires to see if it would affect idle, which it did not. I went on a short ride, and the problem was still there.
When I got back, shut the engine off, and quickly decided to move it, so I started the bike back up right away. I noticed that as I started it, it cranked for a second or two longer than normal before starting, and once started the tach did not respond right away, and instead did another full sweep, then started showing the rpm. I shut the engine off and started it a couple more times, and the tach did this every time. After the third or fourth time doing this, when I pressed the start switch, the engine turned over very slowly, and the headlights were very dim like the battery was dead, and it would not start. As soon as I let off the start switch, the headlights came back on full brightness, and it was as if the battery was fine. Go to start it again, same thing. I did not have a multi meter with me to check the battery voltage.
At that point I called it a night. When I get off work today I'm going to go and pull the tail section off and check the wiring back there by the rectifier and see if I find anything wrong. I'll admit, I know really don't know a whole lot about this kinda stuff