Ill test the charging system with another battery I have laying around. I believe the charging system works fine because it was charging at 14.4v once I was over 3k rpm during my ride, but I don't know what it was doing when my gauge was acting up. I'm going to order a better gauge and I was looking at battery discharge protectors ( I can post a link to one if the forum allows you to). The battery discharge protectors turn off power going out of your battery once your battery drops below a specified point and it will also stop charging your battery once it goes over a specified point.
I'm wondering if my rectifier/regulator possibly fried a connection in the battery (from over charging) and that's what caused the battery to stop charging. I have seen on my voltage gauge the charging system put out 14.6v before when I was at high rpm's, and it may have put out even more since I was at about 10,500rpm.
Also the battery could have not been getting a charge due to a loose connection. When I pulled over I was checking wires going into my reg/rectifier and I pulled one of the wires and it came right out, the wires are hidden under the tank so I couldn't tell if it was even plugged in, in the first place, but that could have been my problem. I guess the only way to tell is connect another battery and check the charging levels.