Bill and all, it's hard to believe that this thread is over 7 years since its last post. But I came upon it when searching for items about the Downeaster and a potential new Portland station.
Bill's experience with the ferry, then named the MS Prince of Fundy, is the same one I got to ride as a teenager on a trip with my parents in the mid-1970's. That operation dissolved not too long after that, and several other operators and vessels have come and go over those years. The last incarnation of a ferry service between Portland, ME and Yarmouth, NS is a catamaran known as HST-2, run by Bay Ferries, and it started just 2 years ago in March 2016. I believe it is still in service, though I don't know if they suspend for the winter.
IIRC the Prince of Fundy was more like a cruise ship than a ferry, in that people had private rooms. The boat made one round trip in 24 hours, with each one way trip about 10 hours long. So one trip was during the day, while the other direction was overnight.
There was also a dock at Bar Harbor, ME where there also were ferries (including the MV Blue Nose) that ran across to Yarmouth, NS. Those also went through a few different operators and ships in their lifetime. However Bar Harbor is well east of Rockport and across a few waterways. To get trains there, it would require a further extension of train tracks beyond Rockport and east to Bar Harbor, something probably impossible.
The reason I bring this all up is that nothing has been done in the interim between the last response to this thread, and this current one, to move the Portland train station. If it were to be moved to where the Portland International Ferry Terminal is, it would definitely open up intermodal possibilities which could help both the ferry and Downeaster ridership as they would feed one another.