Sorry for the newb quesiton but I just bought a whipple off a gentlemen on another forum and he said that I would need to get a lower heat exchanger. Now is a heat exchanger (fluidyne, afco) the same thing as the intercooler?

 

by definition an intercooler is a heat exchanger. The type you're looking for is an air/water intercooler which would fit between the supercharger and lower intake. You could either have one fabricated to fit or buy one

Here is a picture of a whipple sitting on one.