I'm glad it worked out well, BIG. This is the first swap over I ever heard of and sounds like it went well. I really don't know about shift profiles and the tuning of such. I'd try to make a friend at an allison dealer. Maybe there's some tweaking that can be done via software. I know the bigger trannys have retarders on them- you can tell its a big unit hanging off the back. Our wreckers have em. I don't know that the option is for that unit. As far as using an actual exhaust brake, I wouldnt THINK there'd be a problem since the converter would be locked anyway.
I think I understand what youre asking about the shifting. I also try to fool or force the next shift by lifting the pedal. If I feel it's running out of steam, yhea, ill lift to grab the next gear, but you have to ease back into it or else it'll downshift again. You might be able to tune that. I don't know if there's adaptive strategy at play, as in new cars.
I would definitely avoid any hurkey jerkey especially unlocked because you might be hurting sprags in the converter.
What fluid did they put in? Have you been watching temps?