Leigh-
Talk to Tim Comeau. He is always ready to assist any potential 944 Spec racers, and very accessible.
I know little about the waterpumpers, but have you read the rules for the series?
http://www.nasaproracing.com/rules/944challenge.pdf
It looks to me like you can prepare a 944S for the "944 Super Cup" class without changing the engine. I'm not sure about the backdating provisions to change the car into a plain vanilla 944 Spec--more may be required than just the engine--but I'm sure Tim could line you out on that.
My first reaction to such a plan would be to recommend that you just sell the 944S and buy someone else's already completed race car, however. You will probably come out many $$$$ ahead that way, over converting and preparing your present car.
TT