I have the EMP roof (see post #6 in this thread). Adds about 1/2" in overall height.
My first windshield was a Moose folding which had abut a 6 inch gap at the top, nice for my GoPro mount but a real downer in the rain, plus it scratched quite badly, (not sure how the EMP windshield would perform, but I'm sure it would fit perfectly with their roof).
I have since gotten the sxswindshield see:
P500 - Honda 500 Full Glass Windshield which I'm very pleased with, and it fits great with the EMP roof.
If interested call Fred direct at 801-380-1255.
Might be the best solution for your storage issue, roof gun mount may present a slight problem due to your height though.
Check out post #45 for pictures of Fred's windshield installed with my EMP roof, actually the whole thread is worth a read.
He's a member and a great guy to work with.