Yes, it will work but it required a ****LOAD of fabrication and work. You could buy 2 KB blower kits for your Cobra (which is FAAAAR better than the Eaton anyway) for as much as you're going to spend getting the Eaton to work on your car
as it has been said, would require a load of fabrication and not worth it in the end. the 98 cobra uses swirl port heads where there are 2 sets of intake ports per cylinder. the 03/04 cobra uses tumble port heads which have only 1 intake port per cylinder. you might as well just buy a kenne bell for the time and money it'll cost.