Ok, today I spent 10 hours debugging all my problems.
1. The first two boards have pulldowns on /INT1 because my documentation did not show the correct notation, so I thougth it was active high. Changed to pullup and all games started working, real carts, all 64drives etc. 64drive HW2 managed to work even without this because the relatively weak pullups on the cart brought the signal above logic 1 threshold. If the line is stuck low as it was, it would spam the game with interrupt signals and the handler woudl basically spend 99% of the time servicing the interrupt.
2. Same thing on the combined board, but I found that the Rambus Vterm regulator was going into hysteresis, a sawtooth with 0.4V ripple. Since the frequency was 15khz I could even hear it. I foud that because the bulk bypass cap on Vterm was too big for the footprint, it wasn't even touching GND. Fixed, and it booted its onboard 64drive!
Power draw is around 0.56A @ 12V, so about 6-7 watts. Not bad!