When jetting on your own, you really need to set the main jet first. The main is what gives you the best outcome at full throttle but also has a little effect everywhere else. So, first thing to do is set the main and then adjust idle and midrange after that.
There are several posts you should look at before diving in head first.
http://faq.ninja250.org/wiki/Can_I_impr ... jet_kit%3F
(Use this resource... it's awesome. But be sure to check back here for part compatability.) The Ninja and the GZ are very different beasts.
viewtopic.php?f=8&t=15&hilit=rejetting
viewtopic.php?f=9&t=1058&hilit=jetting
viewtopic.php?f=9&t=513&hilit=jetting
viewtopic.php?f=8&t=617