Master shut off switch charging problem

How to fix this?

I would start with some research and by asking myself some questions

That is things like

1....Do I really need a battery at both ends of this car?

2...Do I actually need to disconnect both batteries?

3...Do I need both batteries online for "running" or is one or the other just a booster for STARTING?

If you just want (example) a starting boost, I would solve that by rewiring the front battery back to normal, and feed the rear battery into the starter with a Ford type solenoid activated by the starting circuit, so that when you twist the key, and the OEM starter relay activates the starter---off the front battery, it also brings up the rear battery through the Ford solenoid.

In that case "I would guess" you would need NO disconnect..........just an example