Running in is a period were you carefully run the motor very rich but at as close to normal running temps as possible. This is to bed the piston and sleeve properly so you get peak performance and long life from your motor.
If you just run it hard straight out of the box, you won't get the best performance and it won't last long.
It is normally achieved by putting foil on the cooling head and running around 12 tanks through the motor. Go to page 78 on this forum and near the bottom of the page is a very good run in procedure from one of the Go distributors who posts here. Follow this and you will be cool. Once you have done the 12 tanks tune your motor according to the Massive Mods post on page 131 of this forum. Basically HSN 1/2 a turn in from flush and LSN 2 1/2 turns in from flush. You will get max performance after you have run around 1 to 1 1/2 gal through your motor. The Go motors are very tight when new and take a little fuel through them for the metal pinch to subside, but this makes for a long lasting and good performing motor. Don't forget to heat the motor before starting when it's new or you won't be able to turn it over on the starter box !!! - not easily anyway. Hope this all helps.