the rear could use A LOT of touching up. Get some plexiglass from Lowes (shouldnt be more than $15 for all the panels) and just screw them on there.
As far as the vg's, the roof rack could (and probably is) causing a lot of turbulence in that area so the effect of the vg's there is going to be far less (since they need laminar flow aka smooth flow of air). However, i think they still help but just very little.
Do the underside of the rear, that is going to have a big impact.
Philip1 
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