UPDATE #1: OK, I hooked up the CW-80 into the TIU fixed input 1, and adjusted the voltage to just under running speed (sound and lights still on, steamer).
"Whistle-Bell-Bell-Bell-Bell-Bell" - Nothing
"Whistle-Bell-Bell-Bell-Bell-Bell" - Nothing
"Whistle-Bell-Bell-Bell-Bell-Bell" - Two whistles, the signal that I put it into Conventional!!! Yay!
Now, using the CW-80 throttle, running thru TIU fixed input 1 (and fixed output 1 obviously), I can cycle the engine through NFNR!
You can than shift CW to FIX 2 and test Fixed 2 output. If the engine reads the watchdog and you can run with DCS you have a bad component on FIX1. That is repairable. Than test VAR1 and 2. At that point we have the TIU figured out and most likely the engine.
With the help of banana plugs, shifted CW-80 to FIX2, VAR1, and VAR2, with the Z1000 brick supplying TIU power through the barrel connector "Aux Power Input". Power-cycled everything between each change to another port (to reset the TIU, primarily). No luck.
Repeated "System->DCS Setup->AON", and no luck there (other than killing Variable 1 & 2). Turned Variable 1 & 2 from "On" to "Fixed", and the engine operates conventionally.
Despite all of the steps above, with the engine in neutral, "NO ENGINE FOUND".
Then I moved the Z1000 barrel connector to the Commander, transferred the track wires too, and the steamer runs perfect under DCS.
UPDATE #2: Using the "Whistle-Bell-Bell-Bell-Bell-Bell" several times, I successfully got the diesel into conventional mode. Now, under conventional operation, when track power is applied both engines come up in neutral (NFNR). But, still doesn't respond to TIU DCS.
Moved all wires back to the Commander, and both engines work perfectly.