Some species of pistol shrimp are solitary and don't pair up with gobys. Without a positive ID it is hard to say if it will or not.
As for getting Mr. Goby and shrimp together... Maybe try removing him from the display and keep him in the fuge for a while (weekish)? Once he forgets about his established territory then reintroduce him into the same area as the pistol shrimp. One method I remember reading is using something like this:
http://www.petco.com/product/7449/Lee-s-Multi-Purpose-3-Way-Breeders.aspx and weighting it down. Put the goby in it and leave him by the shrimp burrow for a while. When you release the goby hopefully he will pair with the shrimp.