Wiring problems?

I have a 95 Chevy Cavalier that I had the transmission rebuilt on about a year ago. When I got it back it ran for about a week and then the battery died. We went and bought a new battery for it and it ran for about 3 or 4 days and the battery died again. We charged it and it started right back up and ran for about 2 days. It has been sitting in our backyard for about 9 months doing nothing. A couple days ago we started it up and it ran. We drove it around for about 2 to 3 days and it just now died again. My dad is pretty car savvy and cannot figure this out. He thought it was the alternator but he has replaced that about 4 times. We are pretty sure the shop that rebuilt the transmission rewired it wrong when they put it back together, but my dad cannot figure out what could be wrong. He has gone through the wiring twice and not found anything. Is there any common thing that we could be missing here?