I seem to recall a noticeable improvement in mpg (which to me meant the engine was finally fully broken in) right about 10K miles. In the almost 75K since then, not much change...
If you're concerned about the break-in, I believe the official MamaYama rules are not to exceed 4K rpm for SUSTAINED periods during the 1k break-in period. Doesn't hurt to bounce past and back down.
When I first got my bike, the big discussion was the "motoman" break-in (try the search function), which essentially said wind the fully warmed-up brand new motor to redline in 1st and 2nd and then decel hard - repeat until the engine got a couple bars hotter, then let it all cool completely down, repeat for the first 25 miles or so, and then change your oil. I did a variation of that method (up to about 7,500 RPM - redline just seemed too abusive) and have had no problems - didn't hear of anybody grenading their engine by doing the full Motoman either. Vary your RPMs and DON'T let the bike idle for extended periods and she should be fine.