Mike, regarding the window panel I think it's better to make it adjustable so that after you have the hard top as you like it you can fit the window panel up to it. The manual has you using 2 people, a level and bolting it to the seat belt mounts, but . . .
First, my rear firewall (behind the seats) is fastened by 5 rivnuts across the top - the arrow in this photo is one of the bolts that go into a rivnut. If yours is riveted you can drill out and bolt. Next, I drilled 5 1/4-inch holes in the bottom of the window panel spaced to match the 5 bolts in the top of the firewall, and then elongated the holes in the window panel. Now the window panel fits under the top of the firewall and you can raise the window panel up to tightly meet the ceiling, then tighten the rivnut bolts. Finally, drill the 2 holes for your seatbelt mounts and bolt the belts over the window panel.
firewall window.jpg