How to align a tail gate

From Crankshaft Coalition Wiki

i have a 78 f150 and i'm trying to align the tailgate but there is really no gap for it. I have an aftermarket box that bolts nicely together. The inner/outer fenders are one piece and the floor already pre assembled. But when i bolt it together the tailgate does not have its proper gap and when i align the tail gate to have proper gap i have a 1/4" gap in the floor that looks horrible. If you guys have any suggestions i would love to hear them.