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I've heard of guys doing it before, never seen it done in person though. Save your money though if your thinking about doing it, and just BUY a cobra motor.
Yes it's possible, it's not too big of a hassle but some things are different, some timing equipment... it can be made to work if you have the patience and know-how.
I'd imagine a 99/01 cobra motor to be around $6000, but they're not making them... The Aviator engine is 98% the same, swap the intake manifold, plenum, and throttle body, and you have a 99/01 cobra motor. 03/04 cobra motors are much much more.