Ok, I bring news... and pictures!
First, as mentioned previously I have confirmed beyond the shadow of any doubt that the drive serial number is the only thing that matters when generating a machine ID for these cabinets. I took a drive, blanked it out (seemed to also be required), re-installed the base OS, and the machine ID was exactly the same even though the computer surrounding it was entirely different.
So, I installed the base OS v3.86. Installed the base game pack v3.86. Taito games were missing completely from the menu system (Elevator Action, Zookeeper, etc.). I installed the v3.12 base game pack over the v3.86 just to see what would happen. It was intelligent about the upgrade and only installed the older version of games that didn't previously exist (it left the 3.84 and 3.85 versions of the games that were duplicated).
Essentially, I was back to where I was on my "real cabinet" before disabling the v3.1 games. I noted the same behavior in this build, that v3.1 games would lock up during the attract mode, yet if I entered the game quickly (before the Ultracade menu tried to play the attract movie), it would work fine (then disallow me from exiting the game properly).
So, in a nutshell... Running 3.91.3 or 3.86 of the OS with 3.86 game pack does not show Taito games at all. Running 3.1(2) of the base game pack does not work (all games lock up when the menu tries to play the movies). Installing both 3.86 and 3.12 will work until you try to show the attract movie for a game that was not upgraded to 3.86 (Taito games).
Edit: Also looks like a couple of Gottlieb games are included in the issue.
Here are a few screen shots of the installed game list. Again, even though I got there a bit differently, this list is the same as it was on my real cab when I installed the 3.91.3 OS and 3.12 game pack then upgraded game packs to 3.86.