Someone wrote some controller testing software that runs on the DC. Of course, it won't work until you've already plugged in! I'll see if I can find the link.
If you are careful with your wiring, and use a multimeter to test, the only thing that I'd really worry about is the ground. If any of the other wires are touching or accidentally grounded or whatever, it'll just act like the buttons are being pressed when they are, in fact, not.
The ground is merely "extended" off the controller and into your control panel. Unless you mixed up wires or soldered to something you shouldn't have, there's very little to go wrong. Famous last words!

Anyway, I managed to do it without frying anything and I rewired a LOT of different ways along the way. An incremental approach worked for me (e.g., wire up one button and ground and then test).
Good luck!