As far as I know, fuel pumps can "push" quite well but can't "suck" much. If the pump was mounted at the level of the airbox, it might have trouble raising the fuel to that height when the level in the tanks was low.
I'm afraid I can't comment much on the OEM pump, mine failed (due to water ingress) soon after I did this conversion. Whether the failure was influenced by the new mounting position I can't say, but I doubt it, the pump basically filled with mud through the breather tube.
I replaced the pump with a Facet 40105, mounted on the left hand side of my new battery box, with a couple of bolts welded onto the side of the box. The instructions for the Facet specifically state to mount it below the tank, or as near as possible.
The shape of the Facet makes it fit better than the OEM one did into the space available on my bike, actually.
I'm pretty pleased with this mod, the battery box has survived several rough off roading expeditions, including the Red Kite rally a couple of weeks ago (18th place
) where I was basically going balls-out for 130 miles of dirt. Which used 24 litres of fuel, my worst ever mpg!
The Facet pump has also so far survived being submerged in some pretty dirty water.