98 Becoming the 2004 Beast

I am not for sure, but I think there are several differences. The 96-98s have two distributors whereas the 99 and up have the coil on plug set up. I also think there is a difference in the entire upper intake on these years.
 
You need 99+ 4v tumble port cylinder heads to run the 03 eaton setup. Even then there is a lot involved on putting the 03 setup on a non 03-04 cobra.
I agree with Duane123 on getting a kenne bell. Its designed for a 96-98, will make more power, and a pretty easy install.
 
Yes you can run the 03/04 eaton. But it will be much cheaper to run Kenne Bell and make more hp. I had 03 eaton put on my 99 cobra. if id hadnt been car to car swap it would have been a nightmare. I ended up with new cobra gas tank, new cobra front bumper frame, for intercoller , all the pulleys of new cobra, fuel pump, and dozens of other small items. KrazyKoncepts did the work for me and sold me all the parts for $2500 parts $500 labor. They lost money in the install but as far as i know mine was teh first older cobra to have that swap done. with Diablo tune was 430 rwhp on a ver conservative tune. I think if they did it again they said the swap would total out about $7k
Your really beter off going with the Kenne bell set up. will go on easier and probably make more power.
 
fast99cobra said:
Yes you can run the 03/04 eaton

The lower intake manifold/intercooler of the 03/04 eaton will not bolt up to 93-98 4v B heads. So unless you fab up a custom lower manifold for bolting up to B heads you will not be able to put the stock 03/04 eaton setup on.