The funny part is I already had your site bookmarked, it's hell getting old.
About the drive set up, I thought about using a belt drive system. There are several in use in Cmdr Robert Bebe's original "Voyaging Under Power" for far larger and higher horsepower yachts. The idea is to have a "breakaway" area in the drive train that will hopefully stall before wrecking anything important if a solid object is sucked into the prop. The engine could sit lower and along the center line and still keep the prop shaft at the specified angle.
Along that line what about a controllable pitch prop? I am not sure of the cost of one like a Hundested but it would be handy to be able to reverse direction without shifting and to be able to adjust RPM and thrust.
One of the Rescue Minor owners mentioned weed build up between the rudder and rudder strap. What if the strap were floating, with a small gap between the rudder post and strap. It would still deflect larger objects but hopefully allow weeds and rope to pass through.