Well, Ford had "been there, done that" with the 302 and 351 Windsors with pretty good results.
I believe Ford's biggest mistake with the Modular was the tight bore spacing, brought on by a compromise to fit the new V8 into FWD cars. Had the 4.6L bore been larger, like the old 302, the 5.4L wouldn't have been such an extremely under-square design.