I'm new to this whole Pinball thing, but I've got 30 years experience working with PLCs and realtime control systems.
I HATE(!) cutting existing cables. Once you start hacking something up, you introduce new, unknown problems. And you can't easily go back and uncut the cables.
If I wanted to tackle this, I'd remove the main board in the cabinet, get a new piece of plywood and see if I could get the pin connectors that connect the main board to the coin mech, PF and BackBox. Keep the all those parts at 24VAC.
The pin connectors then become your interface point. The coin mech is an Input device, the PF an I/O device and the back box an output device. Put your CPU and your 24VAC IO on the main board and connect them to the pin connector.
The advantage to this is that when (not IF!) you screw up, you can throw in the old main board and re-discover how the system should work. Also, if you want to sell the machine, you can sell it with the old board and keep your CPU system for a future project.