First off, CONGRATULATIONS!
Second, Tim is in the process of reworking his webpage and adding a bunch more FAQ's but for now read through this page http://www.msu.edu/~lyonro/tovaxinhst.html
The webpage is something I slapped together pretty quickly, but if I remember correctly, the questions I asked Tim were just about the same ones you're asking.
If I understand correctly, everyone produces mrtc's, not just people with MS. The difference is that for some reason the systems of people with MS don't keep the mrtc's under control.
Because everyone produces mrtc's, everyone with MS produces mrtc's. From what I gather, Opexa is able to isolate the mrtc's from everyone who attempts to get into the clinical trial.
It seems a bit of incorrect terminology has been involved by us laypeople when we've talked about mrtc's being detected because mrtc's are detected in everyone. The problem (evidently) arises because with some people so few mrtc's are able to be isolated, or their mrtc's multiply so slowly, that the vaccine can't be created in the necessary time period.
It's conjecture on my part but I suppose a possible future option for those who have been turned down for the Tovaxin trial would be dosing at whatever rate Opexa can produce the vaccine for them....once or twice per year?