According to this
website the outer boards were always 4-1/4" on AD trucks.
There's also a difference in frame width, and accordingly cross sills between 1/2 ton and 3/4 ton pickups. Maybe you have a 1/2 ton bed wood set on a 3/4 ton truck. That would explain the non-aligned rear mounting holes. I originally thought you were referring to that hole in the angle strip on top of the rear sill, but that still may be a problem.
