What would have been cool would be a QR rear axle with a captive spacers and caliper. Done to a few race bikes like this. Makes rear tyre change a breeze.
To put your mind at ease, just carbon fibre with a suitably high temperature resin. Nothing more required, really.
Just what I said above: extra layers of carbon fibre with high temperature resin. I think we beat this one to death now...
Yes, that's how we did it as well. Airbox was to our own design, as there is no such thing for a 1198/1098 engine in a 999 chassis.