Wheels
closing off the wheels will increase temps in the rotor area... how much? I don't know. Getting a better flow under the car could help bring that back, but once again I don't know.
Side Skirts
The side skirts your vehicle has are probably more for looks than anything, so if attaching to the bottom is easier, I would go that way. Actually, you might consider extending your side skirts as car as close to the ground as you can. That's the way they are on cars that have them work. I would not worry about dragging based on that two inches.
Rear Diffusers
These are there to help smooth any irregularities in the flow and direct them into the wake, thus preventing them from scattering. It does help aerodynamics, but I don't know how much we would realize the benefits on our road cars.
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