if your topend is worn you'll just need a piston kit from wiseco, and then have your cylinders bored an dhoned to match the pistons.. If its a good shop, ther'll match one piston to one cylinder and mark it for you, then all you have to do is check ring end gap and throw it together.
Get a clymer manual, it'll tell you how to take it apart and put it back together, as well as what your ring end gap should be. it'll also tell you how much play the rod has in it and in which directions that play should be in.
Before you order piston and such, you could have a machin shop measure you pistons and cylinders and they can tell you whether or not its time for a fresh topend if they know what the piston to cylinder clearance is supposed to be.
If you do need a topend make sure you get the needle bearing for the smallend of the connecting rod, where the wristpins and such goes, they don't come with the piston kits for some reason. And get a complete topend gasket kit.
I should've asked this before but....what year is your bike and how many hours do you think are on it? do you know if it has had any rebuilds doneto it in the past?
before you take it all apart you can fire it up with the clutch cover and timing cover off so you can better tell where the noize is coming from.