Hmmm...Let's see...
If Carroll Shelby (or his agents) is/are putting 351's in some of the CSX 4000 replicas, does that mean they're not "real"? Can the same CSX 4000 car alternate between "real" and, what, "unreal" or "fake" from day to day, depending on whether it has a big block or a small block? Does it have to be a 427/428 to be "real"? How about a 390? Or a 352??? Well, heck, they're big blocks, too.
Come on: get real!
It's your car; build what YOU want.
If money's no object and you decide you want to replicate the originals as closely as possible, the decisions are pretty obvious. If you love Cobras (real and unreal) but don't have unlimited resources, you'll have to sacrifice something and it's up to you to decide where you'll have to cut corners. In any case, don't use that $9000 motor for a doorstop, as somebody will be glad to put it in his Cobra!