I'd be looking for any excessive blow by as they are supercharged. Check that the intercooler pump is working(easy, open the little tank on the passenger side of the fan shroud and see if water is flowing around), state of the transmission(the 4R100 is good, but if it's been beat on for years, it may need some love), does the Overdrive switch work(easy fix if it doesn't), suspension is probably tired at that point, again, easy fix. That's about all I can think of off the top of my head.
I have a 2002 HD with plenty of work done, so if you have any questions, don't hesitate to shoot me a PM. Not sure where you are in CA, but I'm in SoCal, OC area.