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If your fluid looks good and doesn't smell burnt I would lean towards an electrical issue. Whenever a customer with an Allison comes in with transmission complaints I rarely suspect a transmission failure, most of the time it's either wiring related or speed sensor related. I can often find it by graphing data and finding the glitch. Your codes would point towards something going on with the speed sensor mounted on the transfer case. I doubt the shop replaced it when they installed the new transfer case. With the Allison, a complete failure is last on my list.
 

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Thanks for the advice. Something to check out. Anything specific to look at on graphs? I have an autel scanner that gives me real time data. It isn't throwing codes at the moment. It only threw codes when it shit the bed before the transfer case was replaced. Has ran fine for 2000+ miles since then with no codes.
I would look at transmission input and output speed sensor data while the issue is happening, have the data graphing and wiggle the wires and connectors while watching for drop outs or to see if anything weird happens.
 
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