Have cooling problem on my Cooper S !

I had the gears that drive the Waterpump that are inside the supercharger go bad. They rattled and then stripped. The waterpump stopped turning and the car overheated. I got it to my dealer and then had a new Supercharger installed. (I had to pay becase I made mods to the car and they said I violated the warranty. Last mod was 15% Supercharger pully.)

Now with the new part installed (with the 15% reduced pully), car runs great again but 2 days after I got it back, and after driving it at fast highway speeds, it overheated again. I can drive it slower on highway and it seems ok, but now it overheats when I get off the highway and slowdown or have to stop at a red light.

I'm confused. Anyone with a suggestion about where to start looking?