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.