For every person I have ever spoke with about this topic I have gotten a different answer.
I have always used the following method for breaking in my top ends. It is pretty simple, but I haven't run into a problem doing it this way yet and I have built quite a few motors. During the assembly process I use liberal amounts of 2 stroke oil to insure that everything is lubed up well for the initial startup. I then mix a fresh batch of gas the exact same as whatever I normally run in the bike. I leave the jetting the same as it was previously as well (provided it didn't burn down from being too lean). I start it and let it run for a few minutes to bring the motor up to operating temperature. Then I shut it off and let it cool a little. At that point I get on it and ride it around the block taking it somewhat easy (no full bore, shift at redline stuff). If the motor hasn't had problems by that point they aren't going to. Check the coolant level and get on it and ride.
If this is a brand new bike, brand new cylinders, or a real wild combo, I would probably suggest taking it easier to start with. New stuff needs to be heat cycled properly in order to allow the casting to relax. If they are beat on too early there will be problems. I've used the above method on bikes, sleds, quads, etc. with used, heat cycled cylinders with good luck but haven't owned enough new stuff to really worry about the castings. Also note that I run my premix quads and bikes at 32:1 and sleds with injection at ~50:1 so this may be richer than many of you guys run.
Just my $.02