Brakes issues appear to have corrected themselves, along with the rubbing sound.. it just went away during one of my 50 mile trips I guess. When I first got the truck back, the pedal went to the floor with the engine off... but after a few times of turning it on, traveling, and having the ABS light come on, they are firm again (well firm in the context of a gmt400 - they still suck).
ABS light has to do with the gear change, from what I gather.
Could I do it over again; I'd throw the warranty out the window and go with 5.13s.. at least that's how I currently feel.