Kobra,
If you ask 10 people how you break in a new, or newly rebuilt engine, you would get 9 different answers. "Tis the nature of the beast. Lets not even consider the dry vs wet cylinder/piston debate.
Most knowledgeable motorcycle owners, shadetree mechanics & tinkerers have their own way of breaking in a new machine. Back when I was MXing full time, I broke them in during practice just before the race. Never, NEVER had an issue with longevity. Now that I know a little more than I did back then, and especially with street bikes, obviously I do not break in on a track. Couple heat cycles, couple short rides and then ride it like you stole it. Yes this is a cliff notes version of what I do, it certainly more involved than that.
I guess the cliff notes version of this post is that break in is a very sacrilegious experience, and peeps break in as they see fit, either by choice or because of lack of knowledge.
Good luck in your break in when it becomes that time!