Please post pictures, that will really help.
The lip seals produce some rotational friction, but the packings will make it near impossible to turn without a wrench. With the packings removed, you should be able to turn it without any sticking points.
The packings should be leaking about one drop every ten seconds. This is how the packings are cooled and lubricated. Leaking too much can cause problems, but not leaking at all will burn up the packings and the shaft.
You will need over 700 horsepower to spin an American Turbine stainless A impeller 6000 RPM. Stick with what you have now until you have the budget for the pump and the horsepower.
Yes, adding a shoe and ride plate will help the overall performance of your boat. That is a winter project because you will need to remove the intake to be machined for the shoe. I would say that is a good project for your mill if you are up for the challenge. I can help you with all of that.
The transom cover is something that I really need to see pictures of. If it is really hanging below keel, it is scrubbing off a lot of speed. That would be highly unusual.
Transom plates would be another good project for your mill. You would make one main plate from 3/16" or 1/4" that will cover the majority of the opening. This plate will be permanently installed and should have an opening only large enough for the suction housing to be easily removed and installed. This main plate will also have the steering, lines for cooling and diverter, and anything else that you don't want to drill through the fiberglass for.
You will then fabricate two small plates to seal the main plate to the suction housing. These plates can be fabricated out of 18ga - 20ga aluminum. You will want about 1/8" gap all around the jet, so the plates don't wear into the suction or intake. Seal everything with a generous bead of 100% silicone.
