[kamocat]

The trouble with using AC decoupling capacitors is that they only work on an oscilating signal. Limit switches and potentiometers are often very constant.
I suppose you could put opto-isolators on the limit switch inputs and the coast/brake.
Potentiometers, however, I would expect to be noise-resistant. You could still put a op-amp inline if you want.

To answer my own question, the 3.3v power supply has about 15.5 mA of load on it, assuming the break/coast jumper and JTAG aren't shorted.
The 5v power supply has the 3.3v power supply, plus another 193mA of load.
(The actual loads may be less than what I've calculated; I used the maximum current draw. This assumes the encoder input is not shorted)