Oh, I see. So the first three gears aren't long enough? When you ride, what RPM range do you use in the first 3 gears? When I got my Ninja, I made the mistake of riding it like my KLE. The KLE rode like a tractor, you had to keep the RPM low, because that's were all the torque was. The Ninja is different. You have to keep the RPM between 5,000 and 9,000 to get the best out of it, that's where the engine is most comfortable. It took me a long time to get used too it. At high RPM, there is less wear on the engine, and it doesn't need to work as hard. If that doesn't help, you could change the rear sprocket down a tooth or two, or the front sprocket up a tooth. That should help a little. 

 As a side note, I stay in 2nd gear all the way up to about 45kph, then 3rd gear up to about  65-70kph. Around town in traffic, I usually stay in 1st and 2nd. Remember your throttle control, and use rev-matching and engine braking where possible. It is bred from a sports bike, so it can need very precise throttle control at higher RPM.