Mucho Thanks to Chris Palomarez who sacrificed the better part of a Saturday to DCC a Proto 2000 SD9. We used a Digitrax DH163D decoder and a voltage regulator to churn out 1.35v for all the function outputs.
F0 - headlight
F1 - front dual clear gyralite
F2 - red gyralites (front and rear)
F3 - ground lights above front truck
F4 - rear dual clear gyralite

DISCLAIMER - DO NOT ASSUME that the instructions here are correct. We will NOT be held responsible for any errors, or if you fry your decoder/melt your locomotive or any other damages that may occur. You are doing this at YOUR OWN RISK.

Component List:
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Digitrax DH163D decoder
LM317T Voltage regulator with 4-40 Jameco Voltage regulator heatsink mounting kit. (overkill maybe on the mounting kit)
Use 4-40 tap from OSH.
Miniatronics 1.5v 30ma bulbs
Radio Shack General Purpose IC PC board (catalog #276-150a) - cut up into little bits/chiclets.

SP 4408 voltage regulator settings
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1) 22 ohm on negative (left side)
2) 270 ohm Surface mount across negative (on left) to output (center).
3) Test with 1.5v 30ma miniatronics bulb across negative and outputs.
4) That combination equals 1.35 vdc out! = perfect brightness!
Function chiclet cards get NO resistors.. lights look good already!
Time to wire da baby on up!

Also added ground lights above front truck..

Oh, and we discarded the stock P2K light board entirely.

DISCLAIMER - DO NOT ASSUME that the instructions above are correct. We will NOT be held responsible for any errors, or if you fry your decoder/melt your locomotive or any other damages that may occur. You are doing this at YOUR OWN RISK.