H20 seal or leaky HG
If it were mine, I'd wanna know if the seal went bad or if the lack of head bolt torque at the factory has led to leaky head gasket(s). Do a pressure test on the water system AND a leakdown test before changing out the water pump shaft/seal. While performing the leakdown, pull the rad cap and have a listen for hissing air, indicating a breached head gasket. Pressurize the radiator with a radiator/cap pressure tester and listen at water pump impeller and then at the spark plug holes, the exhaust pipes and crackcase breathers. This should indicate where the leak is.
After 9k miles, my 2004 was pushing water out the overflow when I gave it the beans due to the combustion pressure. It needed the head bolt and washer TSB. My dealer, Scuderia is peach and did the job under warranty on a 6 year old bike. I got lucky and the leak hasn't returned (7k miles so far). If yours has leaked and let some water into the oil past the head gasket, the symptoms could look like a water pump seal.