Actually I could put the top back on.
After I cut the top off, I cut an extra 1/4" off of each cut on the roof section. Then I plated, with sheet metal, all of the surfaces being careful to try and make them match up as best as possible. I also welded a strip on the windshield side that overlaped the roof section about 1/2". This was kind of a wind deflecter, to keep wind driven water from the joint.
I built small brackets, one with a nut welded on it, and the other had a hole for the bolt (one for the roof mount, and one for the cab side).
I used 4 across the windshield, and about 4 more across the back. I sealed it with self adhesive camper shell weather strip.
The more time you take to make the seam at the windshield fit perfect, the less likely you'll have leaks.
If you are going to do this to a standard cab truck, you may want to pick up a "mini truckin" mag. There still might be companies building the convertable kits. Costs a little more money, but they are a lot faster to install and generally are a better finished product.
The only place I usually had a prob with leaking was at each side of the roof, by the doors. Sometimes I would just run a small bead of silicone across the whole top seam for the winter, then cut it and clean it off in the spring.