I replaced my waterpump last july, it was leaking coolant from the weep hole which, as I recall, signals a dead waterpump. Rode the bike for at least a couple thousand miles since then with no problems but a couple days ago I saw a small puddle of oil under the bike. Poked around and saw evidence of leaking from two spots: the airbox breather, which doesn't seem to make sense because my oil is nowhere near over-filled; and from the waterpump- not from the weep hole, but from the part that slides into the engine. Which also doesn't make that much sense to me because I would think that if I damaged that seal while installing it, it would have leaked sooner, and also as I recall that goes into a water passage rather than an oil passage.

What do you guys think? I could easily be mistaken about the source of the leak, I haven't had time to take off any plastics. The bike has somewhere around 60,000 miles. I have replaced the neutral safety switch which leaked in the past. I did not replace any other seals except on that metal coolant tube when I did the waterpump in July (or, if I did, I don't remember doing it).

Carefully run your finger under the clutch piston housing.  Careful, cuz it can be sharp.  Is it oily?  That would indicate the seal on the clutch rod is leaking.

Airbox wise, I'd just clean it up and see if it comes back.  They do that on occasion.

I've also seen the shifter shaft seal leak. 

Oil finding trick, since gravity can fool you where it came from.  Degrease and wash off the oil, let it dry, then put footspray (tinactin, etc) or powder in the general areas of the leak.  Start her up... you should see the white stuff bleed when the oil start coming out.

Mark