It's been three years... time for an update!
Within a month of use, the 1/8" glass shattered, and the cabinet went back to the garage. Whatever you think, trust me: 1/8" is NOT thick enough for cabinet glass! I replaced it with a sheet of 1/8" clear acrylic plastic. Cutting this is a different experience, one I didn't do so well on, but it's a heck of a lot safer. Since then it's held up well, so I'm happy. It seems to hold scratches more than I'd like though.
The 10gb HDD had to go, and preferably before it crapped out and lost my hard-earned setup. I bought a cheap CF-to-IDE adapter off eBay and a 2gb CF card. Once again DOS turned out to be a huge mega pain in the butt. Hours of fiddling, attempting to install the latest FreeDOS, trying out AdvanceMame, black screens, lockups, reboots, etc etc later - oh the hell with it, I just gave in and cloned the 10gb drive over to the 2gb card, since it was at least a working setup. I did manage to pull in a few improvements though: recompiled DosMAME for Athlon with a couple bugfixes, and a few new ROMs, notably Atari Cocktail Tetris!
Pulled most of the RAM out, leaving just 128mb. This prevents me from loading some of the largest ROMs (Rockn' Tread series, Tenkomori Shooting) - you know, the stuff that doesn't run on the cabinet anyway. Journey still plays despite the 49mb .wav sample, so I'd say I have enough now. The rest is going to a different board for a different project.