*the little voice in my head thinks that the rear tire spats will trigger flow separation which will overshoot the actual outer edge of the flap,leading to turbulence of such a degree that you'll risk re-attachment downstream.
If there's any way you could tuft that whole area and get a friend to watch,photograph,or videograph,you could see what's happening there.
If you blended the spat into the rocker panel,as Subaru did with their 1986 XT (Cd 0.29) you could kill any turbulence formation.
*As to the gap behind the rear wheels,yes,seal those areas,after checking out 'diffusers',which you might integrate into your design.These add a premium flow component to the wake area,and later,if you do any boat-tailing,it will pay you extra dividends.
