Engine breakin w/tuned pipe, or without?
I tear down my new engines as well. Some will say it's a waste of time because the manufacturer's warranty will cover any problems that may arise but for me packing up and sending back an engine is a waste of time. Spending a couple of hours on a new engine sure beats waiting a couple of weeks for warranty service.
Another thing I like to do is measure and record the major dimensions such as bore & stroke, bearing dias., port timing,etc. I have a log book I keep this info in. It's a great help when you need bearings or want to try a different carb or want to do some port timing changes.
GUNSHIPGUNNER - do you use any software to help you with your engine modifications?