Been on 100mg of minocycline a day for 3 months now. How long can I stay on this? Any side effects from bring on so long?

Maybe. Long term abx can cause a few things to happen. As the number ; kind of bacteria in your GI tract change, it can cause diarrhea etc. Also, it selects resistant bacteria: all that are susceptible die out, and the ones that aren't proliferate. That said, many infection-causing bacteria are already resistant to tetracyclines. Most ppl can take Minocycline for years w/o any major side effects.