As for auditing my roms? Well PinMAME uses the MAME core, so why not use Romcenter (or ClrMAMEPro if you like it instead) and have it create a DAT file using PinMAME's EXE?
It worked like a charm and I was able to clean up my pinball roms. You MUST use PinMAMEW though, NOT Visual PinMAME, to generate the DAT file. Visual PinMAME works a little differently and uses a DLL for it's core instead of an EXE.
Hope this helps anyone who has been wondering how to keep a handle on their tables and roms.
P.S. I'm starting work on my own table. I can't tell you it's theme, it's never been done before.