And from what I understand, when CSX hands over Beacon Yard to Harvard, the MBTA will be able to double track that brief single track section.
Are there any other portions of the line that are similarly bottlenecked by single tracking?
No, the Worcester Line is fully double-tracked except for that 1/2 mile where the yard leads cannibalized some of the former mainline tracks. That's a really easy fix involving upgrade of the first yard lead next to the mainline to full passenger speeds, and a little reconfiguration of switches to retire the yard tracks and consolidate things. Easy enough that they'll do it the second CSX is fully out of there; it's not a significant enough expense that they'd be too strapped to fund it in-house. Their new CSX Worcester yard is proceeding at a brisk pace pretty much on-schedule, so heavy freight ops will probably start to draw down in another year and give the T some schedule openings. The yard might not completely close until 2014, a couple years behind schedule, because their other new/expanded yard in Westborough still hasn't begun construction because of permitting issues that are dragging along painfully slow. They're unlikely to completely shutter Beacon Park until Westborough is done-done just in case disaster strikes on completing that project, but we should start seeing the traffic get lighter and lighter when Worcester's done and the state has completed its bridge-raising work in western and central MA to allow double-stack clearance into Worcester.
As previously noted the CSX dispatching is the main constraint on speeds and passenger ops right now, and that's also waiting on the full completion of the Beacon Park relocation before the dispatching tilts advantage: passenger. I don't know if the T is completely wresting control of the dispatching away from CSX, but at the very least there'll be passenger priority now and enough breathing room opened up to substantially increase schedules. More, actually, than South Station can hold at the moment so dispatching won't be the primary constraint any longer. Most freight will now stop at Worcester and not even enter MBTA territory, with a subset continuing the short distance to Westborough and a smaller subset still continuing to Framingham Yard. Only 1 daily freight--to Everett terminal via the Grand Junction Branch--will still be going to Boston in off-peak hours after Beacon Park is closed.
The last residual bottleneck they have to fix is that the Boston-Framingham segment of the line still runs on old wayside signals, while the rest of the southside and the Framingham-Worcester portion of the line have been operating with cab signals for close to 20 years. Train spacing can be a bit tighter with cab signals, so it's a necessary part of the post-Beacon Park closeout work to fill in that gap on the system's second-busiest commuter rail line if they want to run more trains. Also would prevent any chance of a close call the line had last year when two trains avoided a head-on collision by only a few hundred feet because of a blown wayside stop signal while a stretch of 2nd track was being worked on. That kind of mistake can't really happen with stop-enforced cab signals, which makes it safer to run the kind of tight headways the line badly needs.
Somewhat low-bottleneck but still quite beneficial project that's also due to begin is a road project at Framingham station to eliminate the worst of the line's remaining 4 grade crossings. Traffic queues frequently get backed up onto the tracks at that intersection abutting the tracks, it's a mere couple feet from the station so the gates are down a long time, and it's also mere feet from CSX Framingham Yard and the junction with CSX's major southbound freight line. Real congestion nightmare at peak hours that places some limits on how many rush-hour trains the T can send through there, and has some minor drag effect on train dwell times at Framingham station when the road's hosed with backups. I believe MassHighway has secured mostly-complete funding to begin constructing the road underpass with a targeted 2015 start.