As GRJ stated, "repair or replace?". I would vote for replace. But one last test:
The TMCC Command Base broadcasts its RF signal A) into the outside rails of the track via the track wire connection, and B) into the house wiring ground (green wire). The TMCC receiver in the locomotive senses the RF voltage from the track and the signal emanating from the house wiring.
At this point, the replacement wall wart is powering the Command Base which is responding to the CAB-1 remote (red LED flickers). The ALCO PA-1 is not responding the the TMCC signal. Potential causes: the Command Base may not be transmitting the RF signal; the antenna (house ground connection) is not connected; or the ALCO's TMCC receiver (or antenna inside the engine) may be at fault.
Two TMCC receivers are on hand - the 6-24130 PowerMaster, and the 6-18952 ALCO PA-1 Diesel. We know the ALCO is not responding correctly.
The first test I would run would be to determine if the TMCC Base is transmitting the RF signal to the Powermaster. Does the Powermaster have a flickering green LED that indicates a weak RF signal? If the LED is solid green, set up the PowerMaster to run in conventional mode and determine if it can be commanded using the CAB-1 to control track voltage. If you can verify that the TMCC PowerMaster is receiving the RF signal and responding to TMCC commands, then the ALCO's TMCC receiver/antenna is probably failed.
If the TMCC PowerMaster has a flickering green light and/or is not responding to TMCC commands from the CAB-1, then look at the RF signal broadcast from the Command Base. The signal via the wall wart power connection may not be getting to the house wiring. This can be overcome by connecting a wire to your black/green wires on the wart and running that wire alongside the track and PowerMaster. This provides an "known good" alternative antenna for the TMCC signal (*). If both the PowerMaster (in conventional mode) and ALCO still don't respond, then the Command Base's RF output has likely failed. Replace the Command Base.
If the ALCO's TMCC reception is bad, then I would open up the ALCO and look for a bad antenna connection. The antenna is likely a copper strip hot glued to the underside of the loco's shell with a wire to the electronics. If these have come apart, the loco can't receive TMCC commands.
(*) Another source for the Command Base's RF output is pin 5 of the DB-9 serial connection.
