Tough questions to ask, the answers often even worse when it comes to dealing with the Ford factory rear heat/AC system. I bought a 2005 E-350 people mover and almost immediately went about completely removing the rear AC because I know it to be such a source of problems. The entire case including blower motor, ducting, heater core and evaporator were physically removed as I needed the floor space it all occupied.
The heater was relocated into the raised roof ceiling so I retained the coolant lines. The AC system tubing leading from the front was left intact but I replaced all components (except compressor) that fed the rear evaporator. This was relatively easy I simply replaced the receiver dryer and two hoses.
The problem I had leaving the rear AC intact was when the fragile refrigerant tubing Ford uses is just too prone to developing leaks which disables the front AC as well---its all one continuous circuit.
IMHO removing and replacing the under hood components back to a front-only AC configuration is the better route from a reliability POV. Some have used aftermarket AC lines caps or plugs but they run the possibility of damaging the compressor due oil starvation.
Not sure this is the answer you're looking to hear but its what I did in a similar situation. Here's another thread created about this, my last comment adding some actual part numbers I used. https://www.sportsmobileforum.com/fo...-van-3974.html
Feel free to ask any questions---glad to answer if I can.