I am a newby to Jeep hard tops. When I picked it up from the private seller, he latched the front first, then the bolts. I too had wind noise.
I did just what you said and moved the top towards the rear to establish a better door gap, and fit over the rear body better. I did tighten the body bolts first, then latched. No more noise and no water leaks.
Owners Manual does state to positon top so there is no overhang at the windshield frame. It also states to insatall the top in the reverse order from removal, which would have you tighten bolts first, then latch at windshield.
Amazing what one can learn when reading the OM.
Jean - Wonderful wife
2003 Toyota Sequoia
2005 FA64 (aka LJ) Khaki
Heidi - Golden Retriever/Jeep Dog