You can absolutely drive yourself nuts with the timing, especially if you are trying to take the minocin on an empty stomach twice a day. Eventually I think you will find that you just can't do it in a perfect manner and you need to find a workable schedule.
I take doxy with some food twice a day (the food helps avoid feeling nauseous), but avoid taking it with anything calcium rich (e.g. milk). Then I take all my other stuff (probiotics & supplements) at least a couple of hours after taking the doxy. Its not perfect, but its workable.
If you really need the NSAIDS, you might need to reverse the order (i.e. other stuff first, then minocin a couple of hours after that).
Todd