Well, I can finally close the book on this project. Here's what I did.
Pulled back the liner to expose the fiberglass. With the top on I eyeballed the approximate location where the holes should go and put some painters tape on that area. Put the bolts in the bracket and dipped them in paint. Held the bracket where I thought it should go and pushed it into the top. The painted bolts left two marks where I needed to drill the holes. Drilled some pilot holes and verified that the spacing was good. Drilling the top was very nerveracking as it was at an angle somewhat and was tough to gauge the depth. To obtain the depth required for the wellnuts i had to keep drilling deeper and deeper and was quickly becoming nervous about drilling through to the other side. Just when I was about to stop, the drill punched through.
I pulled the drill out and saw that i had punched through another layer of fiberglass, but not the outer one.
This now gave me enough room to insert the wellnut completely. I used 3M adhesive to re-affix the liner. I glued the flange of the wellnut to the top to give the bolts some bite. Let it dry, threw the bracket up there, tightened her down.
I'm very happy with the results. It drew the bulge down nicely. Wind noise is gone.
I had to adjust the travel stops on the windows since the soft top seals are higher than the hard top seals. (on mine at least)