Well if your sure its pumping air(can you see air bubbles when you run the bike with the radiator cap off before it gets hot?) and the head gasket is good and the heads not warped,why not preassure test the coolant system.Im pretty sure Auto Zone or someplace like that rents/lends a coolant system preassure tester.You should be able to hear the leak if you cant see it,and if it was a water pump seal Im sure your trans fluid would get some coolant in there and turn it white.Does the coolant level go down after the bike sits unridden for a week or so?You could also (or a shop)do a leak down test on your top end.