CafeenMan is right on target. (welcome back, by the way)

I like to control all the variables associated with breaking in a new engine, therefore it goes on the stand. I will not allow an engine to break itself in while flying. Too many variables you can't immediately control. (ie. leaning out when fuel lowers, prop loading/unloading during maneuvers, etc...)

Another reason I run on the stand first, is to insure I have a good engine going into my plane. If I encounter problems after I mount the engine, I know to direct my attention to the tank and plumbing, because the engine has already prooven itself to be good.

Breaking in a new engine often times will require replacing glo plugs. While I'm quite comfortable with dead-sticks; I find it safer to replace plugs while the engine is in the stand.
Minute adjustments are also easier on the stand. I prefer ST engines which allow you to adjust the mid range by rotating the spray bar. I sure would NOT want to do that after the engine has been mounted in the plane. Yes it can usually be done, but why make things harder for yourself?