I've not had to mess around with these relays on mine yet, but looking at the way the lamps are wired back to the relay and control relay, and that one side is effected, I would start with checking the motor ground is good. You say the motor is good, but was it tested in situ, or out of the car with separate power? I would then rig up some long test leads so that I could check continuity in the four wires going back to the relay. A bit of a pain I know, but a process of elimination is usually the best course of action - I've lost track of how many times I have got led up the garden path by diving in without being methodical on electronics
Duncs
IMG_7074 by M E, on Flickr