I ran the files through clrmamepro using the PiFBA .dat file on the wiki, but they still would not boot correctly.
However, it is only certain Capcom games so I can live with not having them on there. Especially since other versions are available for MAME4ALL and other emulators. All of my Neo-Geo games (minus Metal Slug 3 for some reason) work wonderfully. I’m happy with that.