... manual control from the dispatcher station to station ...
This is the problem. I think this is the same problem that causes extra delays in the Harverd to Charles section.
(copied from another post) During this latest South Boston fiasco, there should be sub-blocks between stations, if not already, where manual control is needed. For example an additional dispatcher stand halfway between JFK and Andrew, one halfway between Andrew and Broadway, at least three between JFK and North Quincy. Each stand should of course have dispatching for both directions of travel.
If the system can handle only ten of the normal 14 trains per hour then more dispatcher stands are needed. Let's say the previous station is a mile back. If the next train is waiting for clearance at the previous station it will be at least 2 minutes (at about 30 MPH) before it can arrive at the subject station after a train departs. If the next train were waiting halfway to the subject station it will only be about one minute before it arrives following the departure of the previous train. The T cannot say it has done everything it could do unless it has implemented this idea.
Not too long range plans should have at least 2 blocks between Harvard and Central, between Central and Kendall, etc. Same for Broadway through JFK. Instead o just one train waiting open doored in each of those stations respectively during pileups, there would also be trains waiting closed doored in between the stations. This speeds up the recovery when strains start moving again.