I am rather new to all this as well, I have a 2010 F250, I have went through all of the options for the transmission side of the Mild tune & HD300 tune. I not really crazy about any of them, I have had the H&S installed on the truck for 16 months and about 20k miles.
I am getting to the end of the 5 year power train warranty and thought I would re-install the DPF and go back to stock for a few tanks of fuel before taking the truck into the dealership. When I went back to the OEM tune, the transmission did not do the same relearn type hard shifting for the first couple of run, and would lock up the TC in fifth gear at around 1250 RPMS @ 44 mph. which is great for city driving fuel economy...
I have said all of that to say this, I wish that I could keep this OEM stock transmission turn when I get done with the dealership and install the good stuff again...