Question has to be, are you building yourself a car to cruize around in and enjoy, or building something with resale in mind after you've had your fun with it???

If resale is a consideration, then it's a no brainer to stick with the original engine.... The 63 1/2 Fords are rare enough, but with a date code correct FE and a properly done restoration, the value is going to be considerably more with the OEM parts than with the transplant.....