The header on mine sits practically snug to the windshield frame, maybe 3/16" gap. no leaks but a little bit of wind noise at the two front corners. I just turn the radio up and the noise is gone.
When you install the header especially if the temp is cool do it before you snug down the rest of the top. heres a link to the installation guide, not much better than the sheet that comes with the top, the pics don't match what you actually get. the header angle brackets install like the letter V with the bolt from the bottom. this actually pulls the top forward and down when tightening.

http://www.bestop.com/installation_guides/56804.pdf

good luck

 

Trektop update, still love it, no leaks, a bit of wind noise but the weather is getting better, time to take it off for a while.

 

been wondering about that top. Bestop has been getting some pretty bad reports recently about some of their products for JK's. A forum member recently posted a video on his soft upper doors from them and I was pretty amazed at the poor quality and lack of functionality. I hope you have a good experience.