Yeah I know you've gone through a shit load of problems, I feel for you.
From 7 years of experience loading Tunes on the SCT X4, I would try this.
Put the stock Tune back on the Truck.
Remove ground cable from battery.
Take your X4 device and plug into and good working Windows 7 or 10 machine. (7 works better for me)
Remove/delete any Tunes, backup any Tune files on the device if you don't have the originals.
Make sure to rerun a firmware update on the device.
Reload the custom Tune file JDM sent you. And only the one Tune.
Don't move the X4 or USB cable at the time of loading!!!
Connect ground cable and load Tune.
Now when loading the Tune you can not operate anything in the truck, even getting in and out the will active airbag monitors.
I turn off anything, Climate Control, Nav screen, Auto lights off, keep doors closed, etc.
If your not sure of the state of your battery attach a battery charger.
Things will be on and run like, the intercooler pump, sensors, relays, monitors, etc.
I'm sure you have done almost everything I mentioned when you did this a hundred times before.
Just making a check list for you.
At least you can rule out the Tune wasn't loaded correctly.
Let it idle till operating temp without giving gas or at least till the rpms drop to 600-650 in neutral, then drive.
But normally, don't just go out there and blast it right away.
Setting a good learning table with a full drive cycle is key, especially if you're having issues.