From my perspective, I look for a solid body, frame and frame components. You can always swap an engine or tranny.... but the body and the frame are forever. A late model truck (99-2005) shouldn't have excessive rust or damage on any component. If they were bought new and never waxed or the frames not undercoated or "Zeibarted" and the truck was run on roads with a lot of salt usage in the winter... it's problematic. I would offer a low-ball price and if they didn't accept it, walk away. Next I look at the engine for tell-tale leaks and broken components. The seller should be able to produce some evidence he/she has maintained the truck. Other than that... I think if you find a truck with a solid body and frame, not wrecked, and tracks true, you'll be good to go. Like I said above, the engine and transmission are repairable or replaceable. These trucks are really well built and tolerate a modicum of abuse gracefully. I just bought my 7th one... even after I told eveyone on the forum about a month ago that I planned to keep him for awhile, I sold him to my daughter and then bought another exactly like him, same year, 5 spd, 2Liter, etc as he was except this one is navy blue metallic.
Good luck.
Norm