I have a Eaton on my 99 cobra. It was a real pain in the ass for the guys at KrazyKoncepts to do. The then partner Joe Skinner had a stock 03 cobra and wanted to scrap the Eaton in favor of a monster turbo kit (his goal was 1000 hp.) I met him at PIR was oggling over his car, he looked at mine and said he would swap my intake and goodies for his blower for $2500. The swap ended up being very tedious for them but to their credit they got the job done and stood by their work. Let me list some of the major issues as i remeber them.
1) Ford and SVT are of no technical help in the swap- their stance is that it could not be done.
2) They had to swap inner bumpers so that they could mount the intercooler best if you have an 03 bumper too, so that everything lines up.
3) You will need a chip to tune, they used Diablo on mine and ended up trying like 30 tunes before it was complete.
4) Do the blowers on e-bay come with all of the linkages belts and hoses and pulleys? If not you will need to buy those as well, like i said mine was a car to car swap so it was a matter of pull and play. If you have to run to the parts store every couple hours and buy minor items (assuming they can get them or even know what your talking about) you can burn up a lot of time and money there.
5) You will need to upgrade your exhaust I put on Bassani cat back and dissintegrated the factory cats within 200 miles, Then got bbk high flow cats and blew them out, now i run off-road pipes
6) Make sure you get stock pulley not aftermarket, the 99 motor is 9.5:1 the 03 motor is 8.5:1 too much boost before tune = not a good thing
I dont know your technical abilities, mine was done by a custom shop and they still had hard time. I would not try it myself at home. On the upside with the 1st tune and stock pulleys the car made 432 hp / 399 ft.lbs at the wheels. Is very drivable, and makes great conversation piece at strip/ cruises.
Hope this helps you out. Good luck man