Welcome to the board svtstand99.
Your question is a very popular one for "new-to-me" 99 and 01 cobra owners. Unless you are able to score most of the 03/04 Cobra Eaton swap parts for cheap, it'll probably be more cost effective to just buy an aftermarket supercharger system (ie - Vortech, ProCharger, etc) from the get go.
Try the following thread and use the "search" feature of the msg board while using keywords such as "Eaton," "swap," etc. Doing so will yield a few similar threads outlining the Eaton swap process:
2001 Cobra Eaton SC question here!
G'luck.
