As the saying goes around here, I have only the shit-man to thank.
as of about 1pm, I think I have the MMC3 fully grokked. Reading cryptic FCEU source and testing little experimental roms is an irritating substitute for nice documentation, but nice documentation there ain't. The documentation there is, is at least one of (a) in japanese or (b) horrible. Perhaps both, but I don't know enough japanese to tell. I'm amazed that working emulators get written at all.