So I had a chance to dig back into this today and got it figured out. I was seeing a short across C9 when the driver board was installed in the cab but no short when it was on my bench. I powered up the driver board with just J101, J102, J103 and J104 connected and I'm getting a good 5v. When the MPU board is connected to the driver board then I see a short across C9 and no 5v. If I unplug just the power connector at the MPU, I get 5v at the driver board again.
The game was working fine previously but I was having some issues with lights in the backbox not working so I pulled the driver board to see if there were cracked solder joints on the GI header pins. While I had it out I tested C4 and it was measuring 38uf with my ESR so I installed a new 100uf axial cap. That was all I did to it. Reinstalled the driver board and now this is happening.
Then I remembered that I had tightened down some of the mounting screws for the MPU board when I reinstalled the driver board originally. Thinking one or more of the mounting screws was shorting the 5v, I discovered that the top right and the bottom right screws are causing the short since the short goes away if they are removed and the game works fine. There are no wires or anything else under those screws or the board. This is a TwoBits MPU board and it looks like those two screws that have the washers with teeth on them are touching the 5v line when they are screwed in tight.