To me that does not seem like a linkage problem. You might consider clearing the transmission adaptations and going through a relearn. If you have a Gap it might be a good idea to flash the TCU , reset adaptations and relearn. If that fails you might replace the solenoids.

From what I keep reading, having a HP6 transmission completely blow up seems rare. They must be really well built, 200K+ miles really easy. Nice to know that LR did build these trucks with durability in mind, even if the day to day sometimes gets weird.