I just started a new motor, let it idle until the top of the rocker box's got warm and shut her down. While doing this i heard a tapping, is this a bad sign or just part of breaking in a new motor?

 

Tapping = problem somewhere. Could be clearance issue in the rocker boxes depending on your build or a lifter.
Ron

 

Stock cam or hi-lift? Could be what Ron indicated or something as simple as a pushrod out of adjustment if you do have adjustable pushrods. If it is a light tapping, I wouldn't be overly concerned but would try to identify it. If heavy, then cause for concern but still could be a lifter or pushrod.

 

When you say "new motor" what do you mean? Did you build it yourself or was this a package, or ???

I had huge tapping/clacking after I did the cam chain tensioner service and finally tracked most of it down to rocker support block placement.

But I did ride it for ~1800 miles with it sounding like a diesel. Now its way better, not exactly silent, but not a big-rig either.

...gene