Wanted to close out this issue as well. It turned out that the exterior transmission harness that connects all of the sensors to the TCM had frayed in a few spots. A lot of loose wires inside the loom which is hard plastic and there you have it. I ultimately took it an authorized Allison service center and their electronics tech pulled the harness out, fixed one severed 12V power supply line and repaired a bunch of other frayed lines. Then, he wrapped it all in Matco Tera Anti-abrasion tape and reinstalled. Fixed!
Apparently, there are two 12V power supply wires to the TCM in that harness and because one of them was severed, the TCM had a useful voltage/amperage lower than what my battery was providing. Somehow, on that trip, my voltage regulator kicked off and my battery voltage dropped revealing the harness issue and the symptoms that I was seeing on the road. Consequently, the day before I took it in I topped off my batteries and the problem I was experiencing went away even though it was still there.
Aaaand, now I'm a lot smarter on the Allison!
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