I swapped a 460 in place of a 400 on a 1973 LTD... but it was around 25 years ago. Everything stock. I remember cussing Ford, as it seemed like everything that could possibly be different, was. Sure, they both shared the same bellhousing, but that was about it! It was a good thing the boneyard I was dealing with had a parts car for all the little trinkets, or it would have been a major PITA.
But, keep in mind... I was in high school while doing this, so it may not have been quite as big of a deal as I remember. lol But, Ford did seem to change a lot of stuff that they didn't need to when it came to interchanging stuff.