The other thing to remember is that as your aux will be shoving you along at displacement speeds, there will always be water filling up the gap behind your hull faster then the aux can push it out the way.
As your hull is what mine evolved into, there should be enough rake on the transom to not bother if the aux prop does not have a totally clear view ahead. Mine's sat on it's outboard pin, and has never had a problem shoving the boat along. Before I got the current one, I had a short shaft 2 that also worked as long as you didn't walk too far forward in waves - it's prop was above the bottom of the hull!
Where I am going here is do you really
need to cut the transom at all?