I'm assuming you know about the ferry that runs from Portland Maine to Yarmouth. It's an overnight from Portland to Yarmouth, leavse near sundown and gets to Yarmouth early AM, it would get you to the good parts quicker...
PEI was a nice side trip when my riding bud & I did Nova Scotia a few years ago. We happened to be there when the potato plants were blossoming, a nice not overpowering perfume. Lots of potato fields up there, it's 40-50 percent of their income IIRC. You can't miss the PEI potato museum !!! (I'm kidding, although it actually wasn't bad).
Most memorable stop in Nova Scotia was Lunenberg, I'm a sailing nut & there was a tall ships weekend when we were there (12 boats), also the Fisheries of the Atlantic museum was really good (the Bluenose lives there at the museum, unless they're away on a sail). Also enjoyed a couple of days in Halifax. Things were starting to get pretty sparse up around Moncton way.
This years trip is probably going to be the St Laurence seaway ride, like you're planning, without the Nova Scotia or PEI stops (BTDT). A friend that did the ride told us to make sure we plan our stops for gas mileage because there isn't a gas station every 20 miles like down here. His key word was 'desolate' when he was giving my friend the ride report. We're taking tha camping gear JIC, but probably will not use it. Current plans are for July Weeks 2/3 or July weeks 3/4, fluid because of riding buds scheduling.
Good luck & have a good ride !
EDIT
Just re-read subject post, 2 weeks is not enough time unless you plan to spend most of the time in the saddle. We seemed to enjoy Nova Scotia & it's wonderful people more the slower we went...