I definitely gave the ease of "glass" installation consideration, but really couldn't come up with a good, clean solution. My plan with these gussets is to have no "glass" above the gussets. There will just be a sheet-metal filler piece which will reside between the top surface of the flat gusset and the window mounting flange. On the underside of the gusset, I plan to make another small flange that the rear glass will be attached to by rivets and/or adhesive.
If I had the opportunity to do the whole cage again, I would probably move the main hoop forward a few inches, to allow for gusset clearance inside the passenger compartment. However, at this point, I think I'm going to have to live with the difficulty of installing the rear glass.
In terms of the position of the X brace, I still have the ability to move it "uphill" or "downhill". It is only tacked in place. I know what you mean about giving the cage the maximum amount of support. Currently, there is about 3" of tubing from the top of the X brace to the bottom of the plate gusset, and about 10" on the bottom side. The X bars are set up to be at 45 degrees relative to the down bars.
Steve.