Initially, you mentioned the waterpump gasket. Then later you mentioned that you replaced the seal twice. Just so you're not calling an apple a banana, you did replace the waterpump seal that presses in behind the bearing, right? There is a water side and an oil side to the seal.
Also, make sure the white plastic vent elbow is in the top of the case near the rear motor mount. If it's missing, water from splashing through puddles and from washing the bike can get in there.