OK, I'll share a story that happened a few months back.
Guy first asks me about some drive images for a system. I spend a couple hours finding them (had to search a few external HD's to figure out where I stored them), then have to copy them to a memory card to mail to him (he didn't have any...
I’m not familiar with that particular daughtercard, but they usually run code from the PRG1/2 sockets on the card. Seems odd that it would not block access to the ROM bank on the main board… but you have it working, so it must be so. The daughtercard might be interfering with the shared CMOS...
I believe Joe liked to joke that Mark lived in his mom's basement (and is known for using the initials "ASS"), so it would not surprise me that he asked for this dig to be added to the kit.
I made one once for a Ms Pac cabaret (with custom graphics for a Namco Classics Collection board). It was really hard! Getting it evenly heated up with a heat gun without warping was tough. Came out OK though. I did heat up one end a bit too much, resulting in a little warping and a few...
I worked on a T&F cocktail (repaired the K4900) for a friend a little while back. You should be able to adjust the monitor to fill the entire screen. If not, there's something wrong with your monitor.
Doing an A/B comparison between good and bad boards is not really helpful at this point. If you suspect an address decoder chip is faulty, you need to look at its inputs/enable and see if the outputs are behaving accordingly.
Maybe this will help you...
It's not running code.... Isn't the CPU watchdogging? You're going to see all kinds of crazy shit until you sort that out. Start with the CPU and it's access to ROM/RAM.