@fnkngrv Not sure if you are still having trouble but have you checked the /dev/shm/ folder for the runcommand log files? They usually give a good indication with libretro cores as to why things aren't working.
@supercatfooz Update: I just found an HDF file that seems to work fine, making the two .dim files I have obsolete. I'd still like to know if multi-disk mounting is possible for the future, though! (plus it'll help whoever else happens to have this problem)
@Pyjamarama You can save your controller settings for that game or across the whole core. Those options are in the control menu in the hotkey+X retroArch menu, right above where you edit the control inputs.
That's a shame. I was hoping it was something I could fix on my own. I do love my Japanese computers. I'm glad to see that an official Retropie guide for the PC-88 emulator showed up within the past few months at least.