Good that you choose September, parts of the ACA's atlantic coastal route through southern ME can be quite crowded with traffic, tourists, RVs, etc. Don't be afraid to venture inland, away from the traffic. Part of Rt 1 are off limits to bikes, but the ACA route does reroute you anyway so no worries there.
My only thing about lodging is that campsites in Wells, ME seem to be really popular and crowded. My friend and I opted to stay in a hotel the night in Wells because the campsite looked insanely crowded without much privacy from the other campers... YMMV. I would think a lot of campsites that are coastal and in the southern portions might be very popular, might consider reservations if you happen to be by there on a weekend.