In the era of second generation ground-based gravitational wave detectors, short gamma-ray bursts (GRBs) will be among the most promising astrophysical events for joint electromagnetic and gravitational wave observation. A targeted search for gravitational wave compact binary merger signals in coincidence with short GRBs was developed and used to analyze data from the first generation LIGO and Virgo instruments. In this paper, we present improvements to this search that enhance our ability to detect gravitational wave counterparts to short GRBs. Specifically, we introduce an improved method for estimating the gravitational wave background to obtain the event significance required to make detections; implement a method of tiling extended sky regions, as required when searching for signals associated to poorly localized GRBs from Fermi Gamma-ray Burst Monitor or the InterPlanetary Network; and incorporate astrophysical knowledge about the beaming of GRB emission to restrict the search parameter space. We describe the implementation of these enhancements and demonstrate how they improve the ability to observe binary merger gravitational wave signals associated with short GRBs.