> The only question I have is going to be how I'm going to get things into this new > format, and I'm pretty sure I know the answer.
simply split nointro set in separate prg/chr and then run cmpro with the nes.xml file you can get at http://git.redump.net/cgit.cgi/mess/plain/hash/ (right click on nes.xml and save it), to rebuild a set which would work in NES.
then store the files in mess/roms/nes/ and the xml in mess/hash/ and you are done