If I'm reading this correctly, it sounds like you had this issue before you changed the plugs, too?
You won't get barnacles in fresh water, but you can get weeds growing and this won't always come off just by running the boat. I think the first course of action here is to pull it out and do a proper power wash on it. Otherwise, you might be doing all this other stuff for no reason. It doesn't take much growth - even just a thin layer - to cause the problems you're having.
No, the first season I owned the boat, it had the original Champion plugs and it ran in the normal 4400-4800 RPM range. The boat was previously owned by another gentleman who also kept the boat in freshwater year-round.