I finally got some time to pick this back up.
After debating what I wanted to do, I decided to pick up a new diff lock actuator. I figured if I swapped the new actuator in and it still didn't work, it would definitively not be the actuator.
Last night I took out the old actuator and installed the new. I managed to do this without removing anything else, including the exhaust. It was like one of those really annoying puzzles where you have to turn the thing into a million different positions while trying to remove it, but eventually I was able to get the old actuator out between the exhaust pipes. Next I had to pull back my wiring to the diff so I could wire in the new proper connector. I had put the wiring in when the diff was not installed, and definitely didn't put it in thinking I would be pulling it back with the diff installed. Getting to some of the zip ties with cutters was a challenge to say the least. I got it out after some fiddling and rewired the harness with the new connector, re-sleeved it and staked the back with epoxy, and plugged it all in.
To keep from the entire vehicle freaking out over the locker, I had pulled the fuses to the diff ECU so I could flash the vehicle and it wouldnt know it had a locker ECU. I reinstalled these fuses and then ran the whole process through the GAP tool.
From the GAP IID main menu:
1. IIDTool Config > Find ECUs. This will search the car for all the ECUs. Now that the fuses were back in and the ECU was powered, it was found and added to the available config options.
2. Car Configuration > Instrumentation > Rear Differential. Change the value to essentially "on" (it may be called Active or Equipped).
3. Rear Differential > Test. This one both tests the rear diff actuator and calibrates it. I had to contact GAP to get this added to the tool options.
From there, everything was good to go. Now warning lights, no issues. I could pull up the live values for the diff actuator and verify it was alive. I couldn't have completed this project without GAP's help, they were great.
I'll get some better writeup on all this put together.