This does not answer OP's question, but since he is catching the Downeaster, if he is headed to Portland or north along the Maine coast, he should consider the Concord Trailways nonstop service from BOS to Portland. Takes 1:45, picks up at terminals at BOS and the drop off is at the same location as Amtrak in Portland. OP should be able to catch the 5:35 PM bus and be in Portland by 7:45. If not, the 6:35. Pickup time depends on terminal.
The BOS-BON hop seems a tough one given the timing.