My brakes are not operating normally
There is a pulsing when I apply my brakes.
Jack up the front wheel. Spin the wheel and look for rubbing. Apply the front brake ever so slightly to see where it touches first. Mark that part of the wheel. There are 6 allen head bolts holding the front rotor to the wheel. Tighten the two or three bolts closest to the spot on the wheel where the rubbing occurred.
If that doesn't fix it, replace the pads. Note that this is just the $25 E-Z fix. If you have pulsating when you use the brakes, it's almost certainly the rotor, although if you put on a new rotor you should use new brake pads, too, so it's not like you're throwing money away.
Still no luck? It's time to replace the rotor. You can't machine rotors on a motorcycle like you can on a car. They're too thin. Note that normal rubbing of the rotor by the pads is fine; they're designed to do that. However, if you start to get a pulsating or shaking of the bike (usually the front end) when you hit the brakes, then it's serious. And serious money; this is definitely an eBay/junkyard item. New ones are $250 worth of expensive.
My brake pads are grinding.
It is normal for the pads to drag slightly, especially just after replacing them. Excessive grinding can be caused by having the torque link nut too tight, or having the hex nuts that hold the caliper to the caliper mounting bracket too tight. Be sure to correct this before the rotor warps from being overheated.
My rear brakes don't feel right.
The rear caliper on this bike has a single piston. One brake pad is pushed by one piston, the other brake pad just kind of sits there on the other side of the rotor. You only need to push from one side to compress the whole she-bang. (Not exactly true, but really close enough)
Now, unevenly worn pads DO happen. Excessive uneven wear is usually caused by dirty pistons, or (more often in the case of the rear brake) dirty pins. Another potential cause for uneven wear would be neglecting to loosen/tighten the brake torque link bolt when adjusting chain tension.
Most of the following information is also in the replacing brake pads article, with more detail.
1. Unbolt the caliper and remove the brake pads
2. Thoroughly clean everything that is visible with perchlorethelyne-based brake cleaner. Don't get it on your hands. If you do, use lots of moisturizer afterwards. With lanolin.
3. Carefully apply a BIT of pressure to the rear brake lever to push the pistons out. Be careful not to push them all the way out! Temporarily installing ONE pad will help prevent this.
4. Examine the visible portion of the piston for pitting. If it has more than light pitting, it is due for replacement, as it can cause your brakes to gradually loose fluid, and chew away at your dust/fluid seals.
4.b. If you're really thorough, you can remove the piston entirely, but there's always the chance you won't get it back in
5. Clean everything which is now visible. NO dirt whatsoever is allowed on the piston.
6. Inspect the dust seal (you can't see the fluid seal without removing the piston). If it's there and it's not obviously screwed, it's fine.
7. Remove the lid to the rear brake reservoir
8. Push the piston back in. If it's clean and the lid to the reservoir is off, you should be able to do this with your thumbs (push HARD)
9. If for some reason you can't use your thumbs, use a 6" C-clamp and an old brake pad to push the piston back in
10. Install new pads
11. Replace reservoir lid
12. Push back the rubber boots and lubricate the pins with a copper-based brake pin lubricant
13. Reinstall caliper (18 ft-lbs of torque: that's not very tight!!!!!)
14. Pump the rear brake lever until it gets hard
15. Do a few soft stops and a COUPLE of mild panic stops
16. Ride normally for 50-100 miles in the city before worrying about your brakes again (they'll have to bed in)
If you have ever worked on anything with disc brakes, the rear brake on the Ninja 250 is easier and more obvious. Really, it's about as easy as it gets.