Can I ask, have you joined the Maine Island Trail association? I think they might answer most of your questions in terms of difficulty level and crowds... campsites for many of these are reservable. Website is http://www.mita.org
I am frankly a relatively inexperienced paddler, but I know that sea conditions can change radically in the Gulf of Maine, and tidal bore can be surprisingly large (not that far from Bay of Fundy).