I might be a little confused here. Just to clarify...
You successfully do the Factory Reset procedure and successfully set the Installation Mode to one blink Data.
Then at the third step of the 16 Step vehicle programming procedure, the LED flashes Red and never flashes Green?
Might be because the black ground and constant 12v on the module are connected in data mode? The ads diagram shows them not to be needed in data mode. I could disconnect them if that would change anything.
It is an "Either or" thing with D2D or Hardwired. You only plug one harness into that 4 Pin Plug. If you are going D2D it's the harness going to the R/S system. If you go Hardwired, you manually make the Power, Chassis Ground and Ground when Running wire connections plus all the necessary supported connections shown in Red or Black dashed lines. So yes, the Harness provides +12V and Ground and it is the only source for these signals. It appears to be doing that because you are able to Factory Reset and set Install Mode OK.
As for this 4 Pin plug on the ADS AL-CA on the same side of the module as the LED, that should only have the D2D harness going to the CN6 plug of the CM900-as unit.
At this point in the bypass module programming, all the ADS AL-CA needs is the power and ground from that harness, the Pink wire going to the trucks main Ignition wire,
the Yellow Passlock2 wire, the two CAN wires, the SWC Data wire and the three Immobilizer wires all connected to the correct vehicle wires. I am not sure of the sequence but at each turn ON of the ignition key, the bypass module sees it and does one phase of programming. These might be Passlock2, Transponder chip, CAN and SWC Data but probably not in that order ). I would once again double check all the connections to ensure that the proper ADS AL-CA wire goes to the correct vehicle wire.
If everything checks out, my guess would be either a bad ADS AL-CA module ( extremely rare ) or it has the wrong firmware on it.
Soldering is fun!