I ended up redoing the wiring from the sensors to the garage door opener. I was not happy with how the staples were attaching the wires to the the wall. Some of them just were not up to snuff and I decided it would be better to just start over and staple a tie to the wall and then tie the wires on. I just didn't want a repeat of the mystery short.
As for the rest of the electrical issues, it turns out our Invisible Fence was also tripping the circuit breaker. It would happen once, maybe twice a day. I'm not sure why it's doing it. I've replaced the backup battery, but it was still tripping the breaker. I'm pretty sure it's not the outlet it is plugged into, maybe it's the power strip/ surge protector. I hope so, because anything else will require my calling up the fine folks at Invisible Fence and scheduling an appointment.
So for now the fence is off. The dogs haven't quite figured it out yet and I hope they never do.