Measure, measure, measure. Measure everything!, Get it into a shop with a good flat floor, measure floor to frame on each side, Keep notes! Trailing arm to frame, trailing arm to frame at the spring cups, left bottom spring cup to the top right side spring cup and back again.
Measure the front end the same way. It is entirely possible that front suspension may be affecting the bed as well. It is easier to see an issue on the bed because of its relatively long visible horizontal plane compared to the cab.
Don't forget that when she rolled out from the factory the rear was two inches higher than the front, take that into consideration when you make your notes.
After you measure everything on the frame/suspension, start again on the body and look at the relative measurements 'tween the two. You will find the issue.