I did mine with 4-40 button-head stainless socket screws and used nylon washers under the head. I drilled and taped (CAREFULLY!) the door material and simply screwed in the fastener. First, lay out your hole pattern on the window and drill clearance holes. Then use the window as a pattern to locate the mounting holes in the door. You can do the headlight covers this way also.
I like this method because it allows for repair if necessary. All you would need to do is fill the hole with a dab of epoxy, allow it to harden, and redrill and tap. It also requires a very small hole. This gives you more area around the edges of the parent material, both window and fiberglass body, and makes it stronger near the edges. You really don't have a lot of room to work with, especially around the headlight covers and the top of the side windows. I did both my GT40 and SLC this way and the GT40 has had no problems for more than 20 years.
Don't place fasteners in the extreme corners of the Lexan. Leave at least a 1-inch distance to the edge of the Lexan in the other three directions other than the one facing the edge of the window. This will prevent cracking through the mounting hole to two of the edges.
Oh and wait until after the body is fit to its FINAL position before you install windows. NONE of these things want to flex.