What about an increase in noise inside the cab? Are you planning on incorporating a head liner or some type of coating?
For the LJ Safari Cab, I finished the exposed interior fiberglass surfaces with bedliner, and installed a headliner in the roof. There are also strips of carpet along the side below the windows. All of that can be seen in this photo I posted yesterday. It's vey quiet, definitely quieter than a factory LJ hardtop.
In fact because of the headliner, when running with the soft sides instead of the hard sides, with them rolled down on the highway it's about the same noise level as the factory hardtop. That may be hard to believe, but it seems a lot of the noise in the LJ's factory soft top comes from the roof panel drumming in the wind, so eliminating that and replacing it with the hard roof panel with the headliner really brings the noise way down.
Soft sides installed and rolled down (but obviously not on the highway):
BTW in the photo above I'm also running half doors - the combination of the roll-up sides and the half doors is really great on the trails - it's a very open air experience but still with the sun protection and cargo carrying capacity on the roof.
http://opticarmorwindows.com/default.asp
^^These guys make a JK replacement windshield that weighs 13lbs less than the factory windshield. I bet you could save a good amount of weight with some of their other windows.
Weight really isn't a factor since the Safari Cab won't weigh more than a factory top, even in it's heaviest configuration. I'm not a fan of polycarbonate windows, there's really no way to keep them from scratching over time.