If the long block includes the heads, I think the waterpump location is one issue. On 2001 + duratecs, the pump is driven by one of the camshafts. 2000 is a "one only" year for the duratecs and I think AX4N transmissions as well, unfortunately. Maybe you could get a way with swapping the cooling system, but there is still an uncertainty.
I think the era where newer car engines could be easily swapped ended in the 80s. Cars built after that are very specific, especially with all the integrated, electronically controlled components. It can be done, just with a lot of electrical issues; dashboard lights, etc.
There are aftermarket electronic control systems with fuel injection and transmission control, but they cost thousands of dollars and you have to learn how to program them.
P.S. subframe and suspension is probably identical between 00 and 02, and even 96-07, so that part is easy. For rear suspension, a lot of parts are interchangeable even from 86 to 07.
Last edited by sable2000; 10-20-2014 at 06:48 PM.