Sorry that I keep throwing stuff up here, but This is stuff I either did or had planned to do to my ninja.
Have you thought about changing the front sprocket from a 14t to a 15t. After you ride it, you will see what I mean. IMO, the bike needs the 15t sprocket to help keep the shifting and rpm's down. Don't get me wrong, the bike loves the higher rpms, but riding around town or commuting, will get old having to shift from 1st to 2nd before you get to 30mph. The sprocket change will drop your rpm's down 500 or so. Also, it will help with the break-in as they say not to go over 4000rpm which is 35 mph in 6th (I think).
I have a DYI on this if you want it.