I bought a pig tail that plugs into the trailer harness and wired the lights into the tail light connections there. This way there was no cutting of wires on the truck. Only downside is when you tow a trailer your license plate lights won't work on the 4Runner since you have to unplug it for the trailer, but I'm not worried about that and I don't tow very often with the 3rd gen.
For the lights I used some bolts with LEDs in them I got from superbrightleds.