Hey there,
I have one missing part in the Patrol I bought. The previous owner couldn't exactly tell me what it was for (he got the car like that himself) and just put duct tape over it (the cheapest tool ever!)...because there was water getting on the inside of the car.
The two holes are on the co-drivers side and he assumed it might have something to do with the internal recirculation (aircon?) that is used when there's dust on the outside and you don't want to have it inside...i think there should be a hose connecting those two holes.