When peering in to check that the PO didn't do the powervalve shafts backwards...

Sorry, really can't tell a thing by the picture of your exhaust port. You're not looking for "shafts" so much, but you should be able to work the lever by hand and see the exhaust valves moving.

As far as the water pump, you need to remove the clutch cover from the bike, remove the impeller shaft, and push the seal out from the back side with a punch or the like. I would also replace the bearing while your in there. The shaft may also need replacing if it's rough where it mates to the seal. Otherwise you have a leaking seal again in no time.