What is the best way to break in a motor thàt has a whole new top end
I was always told break it in the way you're gonna ride it. Doesn't mean that's the best method but it has always worked for me.
Just make shere you do heat cycles.
Just ride it. Make sure to re-torque the head and cylinder nuts after a little use.
Start it up, let it idle to get warm, check for any loose bolts/nuts and any other issues. If all is good, go for a spin and rev her out, just no long runs. Bring her back, cool down, check all the bolts. then go back out and beat her worse than Q beats his meat.