Help with motorcycle light problem please!

So the other day a friend and I were testing the charging system on the bike because we noticed that it wasn't bringing the battery up to 12 volts when on but was actually charging it enough to keep the bike running. We decided to unhook the bike's battery while it was still running. The bike didn't die so we figured it was running solely on the stator. When he went to give it a little throttle the low beam headlight, nuetral indicator, speedo light, and tail light quit working. Oddly enough the brakelight, tack, highbeam headlight still works. Here's where it get's werid, the headlight low and high are the same bulb and the taillight/brake are the same bulb. I checked to see if the bulb was burned out and it wasn't.

I checked the fuses and they are all good. I think it may be a ground but the guy i was with told me that there's no commoon ground for all of those systems that would allow part of it to work and not the other part. Does anyone know what the problem could be?