it should phsysically fit however you will not get the numbers that 03 cobras make. the heads on the teksid blocked cobras are good, however they arent optimised for blowers like the 03 cobra heads. also the internals will not be able to take the boost as easily as the 03 cobra internals. also you will probably have to convert to a returnless style fuel system.
ya, the eatons arent that great. i just went for a ride in my friends 04 mystichrome coupe. he has a kenne bell 2.2L at 17lbs of boost with a centerforce clutch. that car is amazing. and the power it makes with the kenne bell far surpasses what it had with the eaton. also if you spin the eaton too fast the rotors inside it tend to knock together. the only problem ive heard with the kenne bell directly is that when you run higher boost you need an oil recirculator.
It won't work. The lower intake/intercooler will not bolt up to the 96-98 heads. You would need to swap to 99+ cylinder heads, swap over to an 03 style front cover, all the necessary brackets & pulleys, new alternator, fuel rails, etc.. If you did all of this the boost levels would be limited due to the 9.9:1 compression.