Mark

Spoke  with Teknosha Customer Svc.  Toyota has made all the connections for a brake controller with their factory tow package. The wires from the jumper harness need to be soldered and shrinkwrapped directly to the wires from the Prodigy. Then the jumper harness snaps into the service connector behind the fuse panel and the black Prodigy connector snaps into the back of the Prodigy unit.

Per Teknosha customer svc wiring for a 2003 Tundra w/factory tow package and Jumper Harness:
The Tundra black w/red stripe goes to Prodigy black
The Tundra green is not connected
The Tundra green w/white stripe goes to Prodigy red
The Tundra brown goes to Prodigy white
The Tundra red goes to Prodigy blue

Hope this helps.
Mark