Background:  I purchased a crashed bike and finally got it running again.  Then I noticed the lower end of my engine was making a metallic rattling noise when revved, and the cam chain wasn't the culprit.  I took the lower end (the one part of the bike that scares me) to a guy who found the rod bearings and a rod to be the culprit.  Now my bike has a new rod, and new rod bearings.  Moral of this story is don't buy a crashed bike.

Question:  Now that I have the bike all back together, what should my engine break-in procedure be?  Should I follow the manual's recommendation of keeping the RPMs below 5.5k for 500?  Is that for the bearings or the rings?