If you remove the latch assembly be sure to get it back on exactly how you took it off. If it is misaligned even a little bit your trunk won't close properly. Easiest way to solve your issue without deconstructing the box!
Took my whole trunk apart still no go it fits but won't turn due to just barely hitting the small part of the trunk by the taillight assembly...looks like I'm choppin the boxes corners off. Huge ported box doesn't go well with mustangs trunks who would have guessed