Do you have any codes or otherwise? When I toasted something in the SHO (never found out what) I was getting an underboost condition code, as it would only make 4PSI. I chased a lot other than physically checking turbos and never found anything.
Are you able to put the truck in M to make it hold gear? Would be interesting to see boost with it rev'd out and holding.
You mentioned exhaust, was that done before or after the issue presented? Could be an exhaust pressure issue if it was done afterwards.
Additionally, what tuner do you have (actual device)? The SCT X4 has a CAM reset option, and the TCM can be reset bu doing a fill battery disconnect for ~40 minutes to an hour and then reconnecting. There is a sequence to learn it properly regarding how long to idle, how long to run AC, etc. but I don't know the specifics of it. I would do a KAM reset (you can do that from the SCT X4 device too) and then battery for a full reset.
Additionally, I would check with ford if they moved shift points, or adjusted anything else regarding shifts.