Wilson, I would like to add to what Sarah just said (based on what she said much earlier.
) If you are taking the Minocycline, you don't have to hurry to take anything else. The bacteria is suppressed and is no longer causing damage. Lesions should be healing, according to whatever timetable is natural for your body.
If you kept on taking Minocycline for years, eventually all the bacteria would get flushed out, the metronizidale just hastens the process. Furthermore, as you no doubt know, Minocycline is very safe. Millions of people have taken it for years at an end - it is often given to help heal acne and people just keep on taking it forever.
So it is doubtful that you will have problems with the drug itself and hopefully your MS should also be put into semi-permanent remission for as long as you keep on Minocycline. I would speculate that you also had Chlamydia pneumoniae infections in other parts of your body, which are now also getting better. The other improvements are probably useful ammunition in persuading your doctor to continue giving you prescriptions for Minocycline.
When the time comes for your next MRI, discuss the results with your radiologist yourself and decide for yourself whether it is working or not.