RE: Bachmann 4-4-0 Centennial Spectrum Battery Conversion
Quite frankly, the easiest thing to do in this case is to gut the existing electronics and start fresh. You don't need the wires coming from the rails, so those can be nuked. You needn't worry about the polarity switch, either. You can wire the smoke unit separately if you want to; many people who run battery power don't bother with smoke since it unnecessarily saps battery life. The lights you'll want to wire direct to the R/C control either for directional lighting or simply as a way to see visually that the power's on. The firebox boards are probably the only bit of the origial circuitry that you'd probably end up using, and they can be wired directly into the main power as well. The only thing you'll want to see is if the boards with the LEDs have resistors on them, or if they're on the main board.
If I recall, there are 6 wires running between the loco and the tender; two for the chuff contact (one 2-wire plug) and the 4-wire plug with power from the tender to the locomotive, and power from the control board to the back-up light (if so equipped). The wires to the motor go directly to the control board, so you'll redirect those for the R/C install. What I would do would be to keep the chuff contacts the same, and repurpose the 4-wire plug to carry voltage to the motor and power forward to the control board or to the headlights and firebox lights. I don't mind the headlight being on all the time, and since the 4-4-0 comes with an oil or kerosene lamp, it wouldn't have been turned on and off easily, anyway. Power to the rear light would likely be directional, and run off the R/C board in the tender.