If you do a search you'll find this question has been asked and answered numerous times.
Yes, the Eaton M112 will fit on a '99 Cobra. The problem is all the additional parts from a donor 03/04 you would need to make the swap work. You will end up spending a LOT MORE MONEY getting the Eaton set up on your '99 than just going out and buying a setup that's specifically designed for your particular application. In addition to the supercharger you would need the intercooler, the heat exchanger, the intercooler pump and all associated plumbing. The lower intake, throttle body, MAF, ECM, the hood, and a bunch of other stuff I can't even think of right now.