....the gap in the roof was your real problem. The latch alignment was the symptom. No - wait, maybe it's the other way 'round! Now I'm confused.
There have been a few "gap" threads, and at least one wherein solving the gap problem also (miraculously) solved a latch problem (at least for me
).
Other problem: A loose latch can also be the result of wear on the rubber bumper strips. Strips are secured to the frame, fore and aft, such that when the shell is closed the front portion rests on the strip, which acts to absorb jolts during travel. If overtime a strip becomes nearly, or completely, cut through, then the shell would sit between 1/4 and 1/2" lower when stowed, possibly causing the matching-side loose latch difficulty you are having.
Denny_A