Don't get too hung up on dyno readings, the most important thing is to make sure your bike is running as well as it can. i.e. the air fuel ratio.
Power readings can vary from dyno to dyno.
The 999r motor can be "tuned" to alter peak power and torque to a certain extent by adjusting the cam timing, "please don't try this at home" is the warning that goes with that though.
The 999 motor in my old hat 998r only puts out 134 at the back wheel with open pipes, "race/open pipe" ecu, and cams dialled to standard settings, pipercross in tube filters,
The cam timing as it left the factory was around 5 degress out. Putting it to standard improved the low to mid range.
I know it's running as well as it can on the OEM ECU and that a Powercommander, new chain and sprockets and a new back tyre will make a difference.