I am trying to hang a light that has only two copper wires (just a plain brown cord wire that is split and stripped) to a junction box that has 3 separate power supply lines coming into it. Two lines are coming in through one hole on one side and another on the other side. Each supply line has a white, black and copper ground wire. On one of the power supply lines the previous home owner (who was a builder) cut off the white cord. So there are 5 wires that need to be connected to only two wires (two white and 3 black, plus the copper ground; which I don't think he had connected). There are two swithches for the one light. One on each end of the room. Can anyone tell me what to do with that 3rd black wire?

I'm going to request that this issue be moved to the electrical and lighting forum. You'll find many more electricians to help there.

The wire you are speaking about is it inside the fixture? Also, if you run your fingers lightly along the side of the wire, can you find some raised bumps on one side. The bumps signify that this is the neutral wire. So take a moment and wrap a small amount of white tape around this lead and a small amount of black tape around the other wire to indicate that it is the hot wire.

Its your ceiling I most concerned with. It sounds to me that you might have one source pairing (Black/White- bare) that is fed from the breaker. The other two parings might be "Switch Loops" which carry power from the main feed through one of the switches and returns it to the fixture when the switch is enabled. Can you get a digital pic of the ceiling box and post it here?