You don't
have to remove it to run any kind of programming. It's one of those things that the tuner will have to keep in mind though.
A lot of times in the tuning, transmission pressure is increased during shifts to give a nice solid feel.....that's not too desireable when the
Transcommand is doing the same thing. Being that you have an early Powerstroke, there aren't a lot of things a tuner is going to be able to do to make the
Transcommand....uh..transparent
short of really reducing shift TV pressure and possibly lowering the torque table.