I had a '98 OBS with the same problem. However it was not swapped or anything.
Unfortunately, with electrical issues, it's really hard for the forum to diagnose. Personally, I replaced the alternator, replaced the battery, checked what grounds I could, and then it blew a spark plug out of the head (threads and all). With the various problems, I kind of called it quits and sold the thing.
Start by checking you voltage draw with the car off. If you find that there is a slight draw, start pulling fuses until you find at least the system it could be coming from. Although with the various swaps, it could be a hack job of wiring, with different systems coming off different fuses.
Best of luck though!