This is a really cool mod. Not sure on the windshield attachment points, but for a seal go to napa & have them look in their catalog of weather stripping. They sell a U-channel type with a tube-like seal on the side. Shaped like this: UO ... Napa part# 770-3175. Maybe you could attach it along the front edge of the roof section with the tube facing the into windshield frame to provide a front seal. Not sure how big of a gap you need to fill, but iirc it's about 5/8" hollow tube. If the front edge of the cut piece of top is thin enough to fit in the U, it might/maybe/could work?
I used the stuff to make a rain-gutter on the front section of my Trackers fiberglass hardtop. It's not cheap, but it's a real good quality seal imo.

Hth,
Fuzz

Sounds like the same stuff used on most car trunks. That is what I planned on using for a seal once everything fits the way I want it.

Your last pictures look great.  This is going to be very cool.

The old Broncos tops are bolted onto the top of the windshield frame. That makes it about 1-1/2" taller when the top is mounted. It won't work for a Sammy. You may have to put some type of fastner paralell with top (cam lock?) to make it pull snug to the windshield frame. That would keep it stock hieght and clean. Keeping it water tight is a whole different story.