I don't want to make you nervous but check out my pic. I too had coolant in oil - lots of it, when my sled was new. Dealer told me it was because it was flashed up. I diagnosed it, and repaired it myself in my shop. Since there are so many tuned 998's out there, to this day I doubt the cracked head was due to flashing them up because there would be allot more of them with the issue. Hearing about yours though, makes me wonder. I replaced head (brand new head) and installed head studs and it has been fine ever since. My theory is that my original head got cracked during assembly. When they installed the core plug (it's a pipe thread which means the further in it goes the more outward pressure it exerts!) either they drove it in too far, OR the casting had a flaw and simply cracked when the core plug went in. If you enlarge the pic, you can see a crack about "3 o'clock" on the core plug boss. The crack went down the outside of the core boss and onto the floor of the head. Good news for me was 1) Yamaha/Cat gave me a new head under warranty saying they had never seen another and agreed with my theory, and 2) the new head was available! The bad news for me was all the labor to move all the valves into the new head, re-shim to spec, check valve seal, new valve seals installed, and then all the labor to disassemble the motor and replace head. It's not exactly a Saturday afternoon job!!
Good luck on yours!
P.S I knew since the engine wasn't burning coolant (not white steam or bad smell etc), and there was no oil in the coolant, that the coolant must be entering the oil via the return holes in the head into the sump along with the rest of the oil draining back. The cooling system was not being pressurized by engine compression. I diagnosed it by pressurizing the cooling system with engine not running and with valve cover off. Sure enough, when inspecting the top side of the head with a magnifying glass, there it was - a crack in the left side core plug boss!! I would not have been able to see it with naked eye. It took a magnifying glass. I could see coolant coming out of the crack and running down the top side of the head into the drain-back holes. Mystery solved!!