---(nearly) GREAT NEWS---
Finished wiring everything up, tentatively put in the batteries, used some elastic bands to hold the game cart in place (as system needs to be upside down to test), turned on, got sound, adjusted with volume control, fine, adjusted contrast (Doom 64 is dark), fine; used controls - all fine, apart from the fact I got the joystick mobo the wrong way around so left=right, up=down, etc; easy enough to rectify although it will mean opening the case and doing some basic surgery. Bottom line is that I didn't get the character doing minor side-steps or moving erratically or some directions not working as I had before. All seems fine. I will correct the joystick orientation and then test again.
This at least proves my theory works and is viable. Until I got to this testing stage I had no way to know if I was going to be plagued with cross-talk and interference on the wiring as I had before or not. Seems fine, so far!
I should be able to post more about this later this morning hopefully.
UPDATE:
Problem - gawd, isn't there always at least one?? It looks like I need to make the joysticks able to rotate, a bit like I did before and wanted to avoid. The orientation of the GameCube joystick, N64 joystick and PlayStation joysticks are different. I wired the joysticks in the system in the orientation as per GameCube, hence left=right, up=down, etc - reversed on the N64.
On some controllers, the X axis is on the left and others on the right; the Y axis can be on the top or bottom. Pain. This means I have to make the joysticks able to rotate. I have to work out the best way to do this; unfortunately this will mean cutting the back of the screen+controls casing, I don't have a lot of choice.
This is a bit of a setback and will need some further modding. Joystick rotation is never normally a problem as normally a system is only designed to work with one setup, this project needs to work for many, so is an issue.

Never mind, I will resolve this, just a pain.