It can also be the interference between the interior door panels and the windshield. Either of them can be filed down to make it fit.
It seems like I almost always end up lowering the dash a little bit.
Not the case with the Duster kit, but if the windshield and rear window are molded as one piece, I remove the connecting piece that goes between them, allowing for a more precise fit of each piece.
For stance correction, the front can sometimes be lowered by flipping the spindles or cutting some material off the top of the spindle and adding to the bottom. This can also escalate into having to shave thickness from the wheel wells to make the tires fit!
Like others have said, test fit before paint.