Speaking from the east coast of Canada, I can offer a little advice that may help. September tends to be almost as warm as August here, the shift in temperature is most noticeable in the mornings and evenings but the day time temps are often in the 70s and frequently low 80s. The first two weeks of October things start to cool down more but every year for the last 9 years on the week of October 1st, we have had a birthday bbq for our youngest daughter, every picture includes shorts and tank tops during the daytime but sweaters and such in the evenings when the sun goes down.
On the floor to ceiling windows thing, I say grab those cabins while you can, Carnival is taking them all out and converting them to balconies and I just don't understand, it is awesome to have the floor to ceiling windows. As for the roughness of the water, aside from storms we have found that it is fairly smooth sailing but others who cruise this itinerary may have better advice from their perspective. I'm just thinking from the sailboat perspective that Sept and early October is some of the best lazy sailing off the East Coast.
Hope this helps.