Little Horse: We appreciate your business and take every inquiry and problem very seriously. Generally on the parts we make there is no drilling required to get the proper alignment. Occasionally a hole will be punched wrong or a stake pocket is formed slightly different and minor drilling is required to get them to align. Can you tell if it is just one hole that is wrong or is the pattern drastically off? Sometimes I remove one or two bolts where the stake pocket bolts to the rear sill. If I can get the proper dimension with a bolt out, then that bolt hole is the one that needs to be drilled.
By the way, the rear sill is punched on CNC before forming so it is very accurate. The Stake pockets holes are punched after forming and may have slight errors so if there is a problem, it usually is with the holes in the stake pocket.
Please let us know a little more detail about the problem.
Mar-Ktech