I've got a little bit of inside knowledge of the R56 Mini and what they did to improve the aero over the R50.
Both are stubby little beasts, which doesn't give you a lot to work with, but the simplest things you can do to reduce drag are improve the shielding of the front wheels and better fixing of the separation points on the C-pillars.
The extremely short front overhand means that the air has relatively little 'warning' of the obstructions ahead and so doesn't start turning out of the way very far in front of the car. This means the front wheels are at a very high angle of yaw relative to the airstream that hits them and so you get a lot of drag generated. Fitting deep deflectors in front and slightly inboard of the front wheels helps. Look at those on a 1-series BMW for an example of what i mean. This isn't the best photo but it was the best that Google could find:
http://www.fotos-de-coches.info/foto.../foto-3541.php
At the rear the highly-curved C-pillars cause problems. The newer Mini has a sharper edge moulded into the plastic to effetcively fix the separation point and reduce drag. The one that ended up on the car was much more subtle than the one the aero people wanted, but it looked too ugly to the stylists. By your Milliken reference i'm guessing you've also considered the old Ford Fiesta-style fences/spoiler combination that kind of offsets the perimeter of the rear hatch from the back face of the car by 30mm or so, and therefore both fixes separation and ensures that the low pressure from the trapped vortex thus generated does not act on the back face of the car. If you can modify it that far, then great!
Then, as Trikes said, try covering up as much of the lumpy stuff on the underside as possible or, possibly, deepen the front air dam by 20mm or so (which would also help in the job of better shielding the front wheels, but could also move the lift distribution too much to the front).