Trucked to be Square
There are a number of ways cabs and beds can be out of alignment with each other, with the frame, or with themselves.
1. Cab & bed height can be off (looking from side body lines don't match)
2. Bed is canted sideways (centerline of cab and/or bed are not parallel with each other and/or the frame) or off-center with cab and/or frame (but centerlines are perfectly parallel).
3. Bed is not level with cab side-to-side (maybe it lines up on one side but not the other)
Other problems I've seen
4. Bed is not true/square (looking across from top of tailgate it doesn't line up true with front of bed. . . it's "tweaked"). Could be caused by frame problem or bed supports not welded on correctly (most likely).
Many bed alignment problems can be fixed by simply loosening the 6 bolts holding it to the frame, pushing it to the correct position, then tightening. This will fix #2.
Problem #1: If the cab sits higher than the bed, fix is easy: add spacers between the bed and supports where they bolt together. If the bed sits higher, well it's much more involved. . . it will require adding spacers to the large chassis mounting pads to raise the cab, since the bed cannot be lowered. I don't know how difficult or involved adding spacers and potentially creating problems with door alignment, sealing, steering shaft alignment, etc.
#3 can be fixed using solutions for #1 and/or #2. Same with #4 unless the frame is tweaked.
Hope this helps. In most cases making your truck "straight" isn't that tough, mine is for the most part except the cab sits about 1/3" lower than the bed and will require spacers to the cab. . . something I haven't gotten motivated to do.
Vaughn