What did you hold the fences to the body with? It looks like latex caulk?
Chris,
Awsome work! I believe 4mm - 6mm should be sufficient for a windscreen recess. If in doubt, make it slightly deeper. The windscreen may be dry-fit flush by using small neoprene rubber spacers and when you are satisfied with the fitting, glue the small spacers into place. Fill the resulting void with the urethane windscreen sealant
when attaching the widnscreen.