greetings sir. speaking as someone with a MK2 board that's been nothing but a fucking headache, I might be able to offer you some pointers on what to try.
the first thing to note, according to board repair gurus like channelmanic, that the surface mounted chips on these boards are prone to the legs breaking and other similar anomalies. I can't fix that, and I'm going to assume you can't either, cause you have to be a soldering wizard to fix that.
I used to get CUSTOM CHIP BAD errors on startup as well, along with an assortment of baby crying sounds and other incorrect sounds. the sound board would also return a SOUND IRQ NOT DETECTED error, despite the sound working.
over the years, I've noticed other people have had the same problem, and no amount of messing with it got it to work right. based on my experience with a DK board that would lock up and do other sorts of strange shit, I found that the socketed chips on it had a dark corrosion on them, and after sanding the chip legs the game worked again.
I don't run my MK2 board ever, so I wasn't ever aware of its condition. turns out, the game roms on it (the 3.1 roms, not the graphics or sound roms) actually had a lot of corrosion on them. after sanding them, the Custom Chip problem went away.
another problem cropped up, but I think I fixed that too (one of the socketed CPU chips had a broken socket that wasn't making good contact with the chip -- quick fix was tying a ziptie around it very tight)
the other thing to check of course is your +5 voltage, but I doubt that's the case here -- that would only really cause the game to not boot at all or reset.
if you have any other questions don't hesitate to PM me about them.
