66 engine swap

It's about time to either rebuild my 66 289 Shelby clone or consider a swap to a new engine. I thought a great combo would be to slip in a 03 SVT Cobra motor, maybe with a supercharger, but I haven't heard of anyone swapping in a late model motor like that into such an old car, and don't know how extensive the modifications would be to make it fit. Would it be a better (and simpler) idea to just rebuild that 66 289 to Cobra specs, and maybe add a Paxton supercharger on it? I live in Nevada, and one of the first modifications I was going to do was to put in air conditioning. Vintage air seems to have the most compatible product, but I don't know about how the supercharger belt might interfere or preclude installing the air conditioning compressor. Lots of questions here I know, but I just wanted to get steered somewhat in the right direction before I started this project.