So far as transferring in Boston goes, when I travelled on the Lake Shore, the Portland station attendant literally advised me to use Concord Coach to get to Boston rather than try to make the connection from the Downeaster. If you're traveling light, taking the Orange Line to Back Bay and boarding there is typically the best way to go rather than going to BOS.A few fairly obvious observations:
1) Having to make a connection with less than an hour between scheduled arrival at North Station and scheduled departure at South Station is a recipe for anxiety. Reliably arriving on time is huge!
2) Walking to or from the PTC after dark is unpleasant.
3) Saco has the best train station in Maine.
4) The Downeaster needs to run on Sundays.
5) Be wary of restaurants that say they can fill a to go soup order in 6 minutes or less.