I'll give a different point of view. I've found ceramic pads to do an equal or better job and they do withstand high heat better. Depends if you want to spend $50 a pair for OEs or $100 a pair for ceramics. If your rotors are good then I wouldn't replace them, but you can upgrade those as well.
As far as the trans goes, DO NOT let someone power flush it. Drain and fill. Look up the Allison procedure, but it's drain the pan, refill, unhook cooler hose, start and stop the truck pumping the rest of the old fluid out, adding back the amount pumped out each time until you see fresh fluid. Also replace the spin on filter. Your choice about replacing the screen inside the trans. Probably not necessary as its a coarse screen.