Typically, there's lots of ground wires, but probably the one running from the bridge is what most people would think of. EMG and many others recommend cutting it cause if you go sucking on microphones in the rain it's been known to smoke more than one bassplayer.
Hard question to answer without knowing what pups you've put in and what you've jacked with. Some passive pups are hard to kill, like some of Duncans stuff. If you haven't jacked with anything else, don't, cause at least that narrows the search, assuming everything was fine before the swap. Backtrack what you've done and see if you crossed something up or if there are any wires that may have come loose or gotten crossed in the process. And obviously, make sure it's the bass and not the chord, jack, or amp. Don't assume it's your work till you've double checked the quick stuff. Although highly unlikely it occurred about the same time, stranger things have happened.
