Im not sure on the exact way to get your engine ready to start for the first time, but there are a couple of things you should make sure of before you decide how to break the engine in. Did you replace the cams and lifters? If they are the smae ones used in the engine before rebuild then you should be able to use the break in procedure as described hear,
http://www.mototuneusa.com/break_in_secrets.htm . If you replaced the cams/lifters then find a website specializing in cams (like crane cams or something) and read up on how to break in a cam. Do this first before using mototunes break in procedure and you should be golden. I have used this guys method to much success, from my single cylinder klx 110, to my brothers 8 cyl mustang. His method definately does work, just read the entire article, then read some of the other ones and you should definately have an idea on how to break the engine in. Hope this helped.