That's the whole deal, the later modular transmissions are made with matching dimensions for all of those things mentioned, identical. They have never been mated because Ford added a couple of different bolt holes not used on the SBF, those dowel holes, but kept all six of the original holes(plus changing the starter and moving it upward). It's as simple as choosing the right bolts for length to mate the existing six holes in the block and trans, minus that one nearest to the starter.
I'll find out how "simple" that is when I pull my Lincoln's 302 for the 347, and use that 302 to test fit a 6R80 to it. I'll be able to bolt it together minus the starter if I like, as a first step. Then cut that hole from the block, and look at the controller to run the 6R, mod the trans cross over, the exhaust, driveshafts etc. For a project truck, it's a big first step.