Robbie: The cross sections need to be small due to the speeds involved AND they are relative to the inlet and outlet areas. 2inches tall x40inches wide needs to be some fraction of the inlet area (1/3 to 1/2), with the diffuser exit area being bigger than the inlet. Figure out where you are most limited on cross section and work the other numbers from there. You could add extra fences (like the side skirts) to control/define a smaller throat if needed.
Sleepyhead/Noncones: A flat floor will be easier to construct. I agree the overall layout with the separated fenders will make for some fairly weak body structure, so a simplified and easily prepared floor is going to be useful. Keeping the center of pressure near the CG will make the aero impacts more invisible with varying speeds and allows the tuning to happen at the extremities and be more effective at balance shifts.