Is that what happens when a cross plane motor is swapped in to a GT 350 ?Not seeing that as being a significant problem at all. Should be able to rewire the Voodoo's injectors and spark plugs to suit the Coyote's ECU. The ECU doesn't care where those things are physically located.
Dealing with knock sensing might be a whole 'nother story, though.
I was told the ECU had to be “repinned” .
I had considered doing that when my Voodoo went down and had a 5.2 Cross plane motor on hand but my Ford tech had no idea what I was talking about .