I'm sorry to dig up such an ancient, ancient thread, but I actually got here via a Google search while looking for a solution to this exact problem. I've found a way to do this, so I figured I'd post my solution in case anyone else stumbled across this thread the same way I did.
My method was to actually play the midi files through DOSBox. On the Quest Studios site, there are a bunch of downloadable utilities; among them are DUMP and PLAYMID. These are both DOS programs; download them and load them up in a copy of DOSBox configured to output to Munt. Then use DUMP to send the Sysex file to the emulated MT-32; once that's done, play the file with PLAYMID (though I assume any other DOS-based midi player will work). Munt will retain the patches sent with DUMP when playing the file, since it's all coming from the same DOSBox process, and you'll hear the music with the proper instruments (and see the messages on the emulated LCD).