Have you considered coming out of the super charger inlet with a 90 degree turn that passes through the inner fender and continues to some kind a housing with your air cleaner inside it? It would have access to cooler air from under the fender, while being protected from water and stones being splashed up from the tire.
Sure it another hole in the car, but you could also put a chiller just before the 90 degree bend before going out the fender.