'06 S2R800

found an oil leak at the vertical cylinder head to engine case gasket - 1) is this common? 2) what causes it? 3) how much is it going to cost to fix it?

It's not the breather, already scrutinized and found that out. It's definitely coming from the cylinder head gasket. I also found fuel leaks at the fittings under the tank. These leaks occured while the bike was on it's rearstand in the garage. I'm superannoyed.

Is it still at warranty?

The base gasket has to have the entire topend removed.
Not that difficult, but hope its on someone elses dime
Not sure on the fuel leaks

mine has a small leak on the vert head too.  I'm not even gonna worry about it since it isn't dripping on the floor and I am not loosing any oil.  Just a few drops on the top end here and there. 

While we are on the subject.  Is is possible to put in a thinner top end gasket to get a little more compression?  I like my s2r 800, but wish it had a bit more juice. 

Not sure on the 800's or any of the S*R's, but the 900 doesn't have had gaskets, just a few orings and a machined fit.

Base gaskets come in different thicknesses so you can adjust the squish. A smaller one would raise compression, but not by much.

As stated the 800 has o-rings and a type of labirynth(sp) seal, no head gasket like the 1000ds does.

make sure your fuel leaks are not running down and looking like a head gasket leak, fuel can pick up dirt along the way and look pretty dark.
You can change base gaskets to set your squish clearance, done right = more hp. Done wrong can have the piston hitting the head. If you give yourself at least 1mm clearance you are safe.

If you are the original owner you should have no problem getting the bike warrantied, If you are past the 2 years you still may qualify for a good will warranty. I would ask first.

According to the parts manual it's a base gasket. I'll be taking the bike to the shop soon. I'm the third owner, so I think I can forget about warranty coverage. Bummer.

It should only take them 3ish hours to do the job with little to no parts.

I have done the job in less than 1 hour on race bikes but that gives them plenty of wiggle room to play with.