the problem is Dan, that the factory specs were a
guideline, and the eyeball of the line crew/inspectors was the final decider - if one part didn't immediately fit and look right, they could set it aside and grab another, but wasting time wasn't in the picture .... also the cab/front was assembled on one line, the box on another, the 2 assemblies then dropped onto a completed chassis .... and you have a long box? the design was prolly done for a shortbox, maybe lengthening things introduced a little variation into the mix
laser level to what? the original stance of the truck is a slight rake, the fender line flows around different curves front and back, and there's actually a slight crown to that line on the fender .... the body side bulges out, the bed might have shims/pads under front and back, or not, the new cab mount pieces you used might be slightly different than the originals .... getting the gaps perfect on the front clip may have required the cab to be off a bit .... and on and on
remember that we're dealing with very low cost, mass produced consumer goods here ... workin mens trucks, not precision engineered show machines, I doubt they specified that feature line had to be aligned perfectly - shim up the back of the box to split the difference, don't get an ulcer over it!
Bill