DOT has gotten back to me with some answers.  

As Streetsblog reported Monday, New York City’s Department of Transportation failed to follow through
on a 2004 pledge to build potentially life-saving pedestrian safety
improvements along the Third Avenue corridor where a 4-year-old boy was
run over and killed last Tuesday.

Streetsblog asked DOT why the pedestrian safety recommendations were never implemented despite a March 19, 2004 announcement by DOT Commissioner Iris Weinshall
that DOT would make an "immediate review" of the Third Avenue corridor
and accelerate "$4 million in funding for capital improvements
associated with the Downtown Brooklyn Traffic Calming… from Fiscal
Year 2009 to Fiscal Year 2006."

Here is a reply, from the agency’s press office:

DOT has acted on many of the recommendations of the Downtown Brooklyn Traffic Calming Report since it was published in June 2004 and improved conditions for pedestrians and cyclists. On several streets in Downtown Brooklyn, DOT has reduced the number of travel lanes, added medians and left turn bays, adjusted signal timings, converted one-ways to two-ways and added parking, all to slow vehicles down and discourage through traffic. Miles of bike lanes have been installed, including a physically separated path on Tillary Street. Leading Pedestrian Intervals (LPI) were installed at 9 locations and LPI studies will begin shortly at 3 more intersections.

Capital work was delayed because the construction was more complicated than initially anticipated. Preliminary plans for all 250 recommended neckdowns were completed by DOT in March 2005, but underground utilities issues led to the need for more complex designs. The project has been divided into two phases to be handled by the Department of Design and Construction. The first phase, in the capital plan for fiscal year 2008, is fully funded at $5 million and includes the construction of neckdowns at 101 locations at 43 intersections.

To put the 2008 date in perspective, the public demonstrations that led to the creation of the Downtown Brooklyn Traffic Calming Project began in 1996.