Well I got him. Didn't manage to catch him with the bottle trap, did try several times. I ended up waiting until he was out, and pulled out a few of the rocks in his cave network; the "middle" rocks as it were as he was on one of the far ends. I then removed the far-end rock, goby split. And, the pistol was far, far easier to catch than I'd seen or estimated. He just kind of strolled, looking around as if he were both dumbfouned & lost -- maybe he had no idea what was going on without his goby pal.

Either way, he's going back to the fish store tomorrow, trading him for some coral.

Thanks everyone for the tips/suggestions.