A simple upgrade would be to run water wetter in addition to the normal coolant. Besides that I am not sure if there is any good upgrade for the exchanger. It seems like you could get a custom one made out of aluminum that would both cool better and save weight, but I have not seen one.
I know that some of the guys have switched the saleen supplied intercooler (the part sandwiched between the superchager and lower intake) with a more efficient custom one.
Click on the link in my sig and give Gord a call or send him an email. These are the highest performing HE for the 03 cobras, so it should be good enough for your car.
Chicane has an upgrade of some sort but they have not posted any details on their website. I am interested but will check it out the next time I get to their shop.
If I remember correctly, doesn't the Saleen unit have input and output on the same side of the exchanger? I know the Ford / KB ones have input on one side and output on the other. I will have to crawl under the car to look again.
Well I looked at my car when I had it on the lift today, and it is similar routing to the 2003 cobra, so a heat exchanger should work in a similar fashion.
Edit: On a side note, are the exchangers brass or aluminum stock?