JoeG,
The signal system on most of the Flushing Line dates from the late 1950s (contract S-60) except for the middle track from 33 St to 111 St which dates from 1938-9 (when it was originally signalled, for the World's Fair) and the portion from 111 St to Main St, which dates from 2002-3 (contract S-32702).
The work going on at Hunterspoint Av and Queensboro Plaza are just for the interlockings. A third project, also now under way, replaces the interlocking at 33 St and moves the interlocking from 69 St to 74 St. This is all traditional, relay-based interlockings with space in the respective relay rooms for CBTC equipment in the near (?) future. CBTC is the final phase of signal work for the Flushing Line.