I believe that in the final analysis the angle of the windshield will have to be one that allows the cowl seal to function properly and still maintains some tension on the top. These were never meant to be smooth tight fitting highway cruising soft top vehicles. Flapping is a natural act for a military jeep soft top. Soft top production tolerances are not tight enough to dictate a specific degree angle for the windshield. New soft tops are expected to shrink an approximate dimension in the first year. How they are maintained over the remaining years dictates how much more shrinkage they go through. If 180 pound GI's for 20 years hanging on the top of the windshield as they climbed in and out of these jeeps did no serious harm to the right sides of the windshields I doubt a flapping top will.
Summer tops are an aftermarket thing. The military only ran one heavy weight top specification. I still recall my first ride in a fresh M38A1 in 1955 with the doors and side curtains removed in May. They flapped then and still do.
Keep in mind that the fit of the doors is dictated by the angle of the windshield as well. It is their fit and not the length of the top and it's flap that determine your best windshield angle. If the windshield itself is not bent then the primary angle determination comes for the condition and age of the cowl seal and the adjustment of the two latches.
The top manufacturers like old Whitco and Best Top give you a distance measurement from the top rear edge of the windshield to the to forward, top, edge of the rear tub panel for their tops. With tailgates measure the edge of the tub at the edge of the tailgate on both sides.
Here are the Best Top instruction sheets in PDF. The measurement info is on page 3.
Flat fender =
http://www.bestop.com/images/installati ... /51403.pdf
Round Fender:
http://www.bestop.com/images/installati ... /51405.pdf
Go to Pizzo's page and you'll see that his rodwork dimensions will actually lock in a correct windshield angle by keeping the door' opening verticalrod 90 degrees to the top edge of the tub.
http://www.odcloth.com/rodwork.html