The Harvard Branch RR got a write up in RLHS Bulletin #113 in 1965, author Robert W. Lovett. Original presentation was in Cambridge Historical Society Proceedings, Volume 38, 1961. The RLHS article is about 24 pages and has a sketch of the line from about Gorham and Museum Sts. in Cambridge to end of line on Harvard grounds. Sketched 1940, so there have probably been a few changes.
If you want to locate site of original Fitchburg RR routing and junction location near Union Square, go to B & M RR Historical Society in Lowell, ask for assistance and look for Valuation Plans, Section 36.1, probably maps 1 or 2 (or SL-1 or SL-2). These are 6/30/1914 blueprint copies of how the B & M looked. ( The SL maps have only land parcels and a schedule of ownership, title, etc. There would have been a corresponding track map, but some of the 1914 ones probably fell apart from use. Most maps have both land and track, but SLs were made up for areas with lots of tracks and lots of land parcels.)
Find the map and you'll see a reference or two to the HB plus a slight line relocation of the original Fitchburg main.
I was in charge of B & M property records in 1983 when B & M exited Causeway Street and much of this great material was scheduled to be dumped. I got permission to donate to B & M Historical Society.