House of the Dead- dead boards?

I’m hoping maybe someone can give me some advice on this HOTD cab. Thanks to Gunblade the Polostar monitor is all working and I’ve replaced the broken blue gun, the fluorescent tube and the PSU (the original died after a couple of uses) but now I’m onto looking at the game boards which appear to be dead. 

The internal wiring has been JAMMA’d so I’ve been plugging a spare JAMMA board into it to check the picture and sound are OK. Now that I’m connecting up the HOTD board itself I’m getting a garbled image like below:

Voltages at the filter board are OK, although they have dropped a bit on the way to the I/O board. Looking at the main board all the LEDs are on (and also on the I/O board):

I’ve read all lit up can mean the CPU is knackered so I got a complete spare board set. I decided to try plugging it into the JAMMA set up just to make sure it works and I get the same garbled screen.  So either the replacement boards are DOA or maybe it’s something in the wiring or filter board?

I don’t think it’s the I/O board as I have a spare of that and it didn’t seem to make a difference when hooked up (unless both I/O boards are broken?)

Long term I want to remove the JAMMA wiring and go back to something more original, and also sort out stuff like this, where the wires for the amp have been soldered to the JST pins. 

I’m making progress with the harness that came with the spare board and I think I have everything connected in the right places on the filter board and I/O board now but annoyingly most of the connectors in the cab to things like the start button, coin counter, etc don’t match. It doesn’t feel right to be hacking up this nice harness, so does anyone know if there are places that sell these connectors? Or should I just stop being picky and just attach new connectors to both ends?