Move your handlebars from side to side, full lock to full lock. If you can feel a 'notch' anywhere bewteen full locks, your head bearings are shagged and need replacing. About £60 (about 100 of your American Dollar

) for the bearings!!
Visually check fork leg seals for leaks. If there's a leak, it's a workshop job $$$$s
The clicking noise you describe could be one of two things, both of which are common traits of the Ninja. It's either the pads moving in the calipers, or the clipons moving slightly.
Test the latter by not putting pressure on the bars with your hands when you brake - you don't have to brake *too* hard to test the theory - take the strain by clamping your knees to the tank. (Good practice anyhow). If it clicks, it's your pads, if it doesn't (or it does *with* pressure on the bars) it's the clipons/fork mounts.
There's no easy cure for the pads moving (they all do that, Sir), but you can improve the handlebar click by loosening all the clipon and fork bolts (one at a time!!!), squirting with WD40, and retorque-ing up to spec. It doesn't always work, but it is a genuine cure. It's to do with a groove in the clipon/fork mounting hardware, moving slightly.
Lemme know what it is?
jb