Since you're really starting from scratch with the wiring, I'm confused about the wiring questions in any case. The color of wire to use is the same color you connected to the headlight connection of the Cruise Commander! I actually have a adhoc color convention I use for wiring ERR installations and using the MTH 10-pin steam tether.
- Red: Track Center Rail
- Black: Track Outside Rail
- Yellow: Motor
- White: Motor
- Green: Chuff
- Orange: Headlight
- Blue, Purple: doubled up for Smoke
If you're confused on the other end in the locomotive, your ohmmeter is your friend to find the mating wire.