Well..
Keep the original controller cable wired up for as long as you can. Anything that makes testing easy should be left on as a general rule.
Then, as you trim the board and relocate buttons you can always test it on the gamecube. That way you know its not an issue of power or the dataline.
pots can be annoying. You have 3 wires that need to be wired up right. The ground, the data, and the voltage line. If it does not work, move them around, eventually you will get it right. Smash bros is a quick and easy game to use for testing of pots.