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.