From what i understand the 6.9 and 460 use the same bellhousing. The 6.9 has an adapter ring to mate to the tranny. You also need to think about accessory brackets and fuel lines. Along with all that extra wiring.
Fuel lines will be a piece of cake...Just use a ford inline fuel pump and a regulator if you are running a carb...probably just plug the return line or even utilize it if you are doing an EFI 460...
6.9s aren't my favorite engine so I don't blame you for wanting to swap
You can always use the wanted section here to source all of the parts to do it...I'm sure the guys here got what you are looking for