I found a discussion of the Middlesex & Boston Street Railway on railroad.net and asked if the Lexington-Woburn line ran along Woburn Street. One of the participants provided the perfect confirmation shown below. Not only did the line run that way, there was a stop at the Boston & Maine crossing, now the bikeway crossing, exactly where I saw the rails dug up earlier this week.
Yesterday: 13 miles. This year: 1014.8 miles.
Update: The trench on Woburn Street is filled and partially patched. Large-diameter concrete drain sections are still standing along the street, so you can be sure more excavation is coming.
Today: 6.2 miles. This year: 1021 miles.