Daddycreswell

My son just bought a 2000 4Runner SR5, I am trying to figure out the keyless entry on it. I started by trying to program a couple of remotes that I ordered off Ebay. The locks wouldn't work after hitting them a few times, so this past weekend I changed all 4 actuator motors, locks work perfect now. So I tried to program the fobs again. Unless I am doing it wrong, the locks never cycle like it says they will. So I got to thinking maybe something is unhooked, there is a security light to the left of the steering wheel, I couldn't get it to light up, so I popped it out and the wires had been cut. So where do I go from there? Is there a box under the dash that maybe has been unhooked, if so where would it be and what would I be looking for? Thanks in advance.