By "refuses to boot", do you mean it shows "PLEASE WAIT" but never gets beyond that?

I think the rev 3 ROMs require a different chip for the game to function properly. The display board in particular will have issues if it doesn't have a compatible chip. At least that's what I have observed with my own machine. Mine came with rev 3 ROMs, but when I replaced the original and failing display board with an NOS one from ebay, I never get past please wait.

Did you try replacing the chip? Not sure about the other issues you mention.

*edit* never mind, I reread your post and saw you updated ROM at U4 on the DMD controller, which is what I was thinking of...

There's a thread here where some folks have successfully upgraded: https://pinside.com/pinball/forum/topic/alvin-g-mystery-castle-rev-3-roms-now-available