I have to agree with cff................if it worked in the donor then it should work in the 69. Since this is a computer controlled motor & trans then just making sure all the wiring is correct should fix things. I do know that in some cases with newer motors there is also a theft thing with the computer but any savvy tech guy should be able to figure it out.
Like rs said........what's the problem ford needs to fix?I am skeptical of the shop that's doing this work and you should be as well.