As Nelly mentioned the actual engine number is down on the LHS of the engine (near to where the sidestand bolts onto the cases). It's a big long number (if you have one at all). To tell if you have 999 heads, are the coils plugged into the top of the head in a single coil/spark-plug combined unit with a wire coming out and a small nut holding them in place? If they are, it's got 999 heads. If they're the old chunky coils bolted down on either side of the engine behind the fairings, then it'll more than likely have 998 heads. I've got a 998S motor with 999 heads so have done the "WTF is it" invesitigative work myself
Hmm co-incidence I think I bid on the same bike and missed the end of the auction. Ended up spending considerably more on a red 998. Currently getting used to the sound of the clutch, requested they started every other second hand ducati in the shop to see if they really all sounded like that! Seems like ducati ownership is an introduction to the carbon fibre "bits" market, wife is getting used to recieving parcels that feel like empty boxes....