Years ago I had my truck painted, and then had to go through installing all new side moldings. Its not really that hard, and if you have a two-tone point job you do have a point of reference to keep it lined up. Verify that all the screws they provided are stainless steel, so you don't have to deal with rust streaks later on.
One suggestion I have is to replace the cab mount bushings first, if they are original. The bed sits right on top of the frame (metal on metal), so it does not settle, but the cab is on top of rubber bushings. When I used new poly bushings it raised the cab up and aligned it better with the bed. It also moved the cab up enough to have the floor clear the transfer case (no more vibration; quieter), and to put my TH350 shifter linkage back into proper alignment. I replaced the cab bushings with the truck sitting in the driveway, doing one bushing at a time.
Bruce