Restore factory ac or go aftermarket

Correct. The controls don't know if the AC compressor is there. They just send out 12 V to actuate the compressor clutch, but don't know if there is any current draw.

You can get replacement push-button switches (~$90 ebay). I would keep all the vacuum controls. You should have a hot-water valve in the underhood heater tubing. You can buy replacements, or even work in a cheaper newer design. Factory was a push-pull setup (2 vac hoses), though you might use a spring-return style (1 vac hose).

I wired a relay for the "blower high" position in all my 1960's A's. Otherwise, the push-button and L-M-H switches tend to melt eventually.

Re tranny, there was a later model (999?) that replaced the 904, with taller final gears plus lock-up torque converter (check AllPar site). For your 318, I think you can bolt up an overdrive tranny for a V-8 Magnum engine. People who did so had to rework the floor tunnel. Might be better to swap engine and tranny to get the MPFI.