I'm sure you've guessed by now I am not well versed in automatic transmission technology (and this has been a learning experience- Its broke so let's fix it)
I did read the service manual prior to disassembly and replacement of the overdrive unit. That was the reason for purchasing a rebuilt unit -I lacked the proper tools to safely and correctly repair the unit. During assembly I paused at the shim installation, but having no other shims I danced with the one what brung me. Everthing bolted tight so lets see what happens? (yeah I know dats a lotta work if it don't - still have fingers crossed that Murphy is hiding else where and I intend to run him down).
Yes, I missed the drain down mod although I do remember the issue and reason for it. AS to rough down shifting haven't experienced it yet but, have been trying to go easy on this trans until all is working.
My heart and mind say "aye" to the Allison conversion, but the better half and my wallet say otherwise. To be honest I haven't read the article you referenced (life happens) but I will.
Your repeated reference to "drbt" and a intensive study of the electrical side of the 48re (again the service manual) indicates that a bi-directional scan tool is required so I am working to access such an animal- seems one can exercise some of the signal pins which might prove helpful.
I will be out of town for a couple of weeks so the truck will be put on punishment until I can get back.