To wrap up my situation and for any future searches...
Short version: I elected to go with a re-manufactured transmission. Truck shifts like new and all is good.
Long version: I could only find one person in my local area that was willing to rebuild my transmission, and he would not offer any warranty as I'm whippled. So, I called a few shops that specializes in built transmissions (popular shops on this forum) and inquired about either having them rebuild mine, or purchasing a built 6r80. All three basically stated that for my power level, and desired use a built transmission was a waste of money, and shipping them my transmission for rebuild was not cost effective as there are several re-manufactured options in my area. They all suggested to source a local reman with a warranty. So I did.
Turns out the transmission had been out of my truck before. Whoever reinstalled it decided to leave the top two bell housing bolts out, and broke another bolt and elected to simply thread it lightly (only 2-3 threads left on the bolt) rather than replacing it. There where other signs as well, harness not routed correctly, etc. The previous owner was absolutely not scared of spending money, I don't believe for a minute he went the cheap route or shade tree mechanic. Rather, I think some shop performed a sub-par repair and he didn't know. Especially since the transmission failed again.
I did call Whipple to inquire if I could just put in a new transmission, considering they have their tune on the truck. Whipple stated it was not an issue, no tune update needed.
Going with a re-man gave me a 3yr/100k warranty, covers everything to include labor for removal/reinstallation. Installation went smooth with no issues, I programmed the PCM for the solenoid(s) strategy with Forscan, and erased the adaptive tables. As of now, I've put around 250 miles on the new transmission and it shifts great. I plan to change the transmission fluid/filter somewhere around 5k miles. Not sure if I need to, but hoping for cheap insurance. FordTechMakuloco suggests to change at 30k when new, 30k after that, then 60k thereafter. I most likely won't have the truck that long, but then again who knows.
All I can think of for now, any questions/comments feel free to fire away.