I need some opinions please..

Ok, so i finally decided to finish the chop i started a year ago and hit a snag..I graffed the D pillar onto the C pillar and cut the back hatch in half so the back window would be removable. everthing fits fine except for the bottom. I have a choice, i can seal it from the inside of the hatch, but it will hang over into the bed about 3 inches when its sealed up, but will line up perfectly when its off. or, i can seal it from the outter shell, and it will line up when its on, but then i lose about 3" of my already small bed portion, and the back of the bed wont be lined up with the very rear portion of the bed sides.
as i see it, my only option is to deal with the overhang caused by the removable back window, or fab up a cover for the bed that i can remove if i want... what you guys think?