David:
On open-top cars, the wind is actually 'reversed' more than one would think - Top Gear (an UK TV show about cars) actually had a test to see which car would make a toupee fly away faster, and the wind patterns seemed to prove that - wind is stronger coming from behind, after having "rolled" and accelerated by the window, and hitting the smooth wind on top, thus coming into the car.
When you have a wind-stopper like you have, that phenomena is reduced, and should help immensely in preventing flapping.
However, it isn't easy to do in speedsters without the roll-bar, and the aesthetics on the roll-bar do vary according to personal taste.
I'd say (with no experience) that a heavier material lines on the wind-facing sides, and probably also reinforced 2/3 centimeter lines of said heavier material, forming an "X" or some sort of pattern, should help stabilize the tonneau.