Guilty... I've been calling it a loop for years, as it's possible to start anywhere along the trail, see it all, and end up back where you started.
The ship's shuttles generally (but not always) drop off pax in the area of Quincy Market, roughly in the area near Exit 24B on the map in the link you provided. That's also just a few minutes' walk from the Union Oyster House.
The length of time the trail will take will depend upon whether you go inside the buildings along the way. (Some are free, some have a modest charge.) IMO, Faneuil Hall, the Old State House, and the Old South Meeting House are well worth an interior visit given their ties to the Revolution and their sheer beauty. So is the USS Constitution, if you have time, as is the African Meeting House on the Black Freedom Trail.
Are there any sites in particular at which you'd like to make extended visits along the way? The first three sites I mentioned could easily take two hours combined... then, after lunch, you could continue in any direction.