Whereis the rear master brake cylinder on a 2006 yamaha kodiak 450

SOURCE: tryin to locate clutch master cylinder for Yamahafj 1100 85 model

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SOURCE: 04 Yamaha Yz 125- Rear brake Master cylinder

Are you bleeding it by gravity (flowing down from resevior thru caliper) or forcing the fluid up thru the caliper to the resevior. The latter will get more air out in less time. Simple cheap pump kits are available at you auto dealer and u can use it on your other vehicles.

SOURCE: Rear brake cylinder and bleeding

Relax....KTM's are delicate in this procedure.
First of all make sure that you are using DOT 5.1 brake fluid and not 4 as we use in the Japan models.
Then take the rear caliper in your hands and push the piston all the way in.Then bolt it on its position.
Bolt on the brake hose to the rear caliper tight and leave it loose on the rear master cylinder side (loose but ready to tight it on like half circle loose) and clean up the reservoir completely.
Take a syringe from a pharmacy and a piece of 3mm clear tube.
Start pushing brake fluid in the caliper's loose bleeder until you see fluid coming out fron the hose's loose end on the master cylinder.
The tight the cylinder's bolt and keep pushing fluid until you see it filling up the reservoir.
When you see the reservoir fully filled up, tight the bleeder, take out the syringe and start pressing the brake pedal 15-20 times and the last one keep it down and loose the bleeder (with a tube attached to it and to a bottle) for a sec to relieve the pressure along with any air bubbles.DON'T LIFT THE PEDAL UNTIL YOU HAVE TIGHT BACK THE BLEEDER or the system will **** air in.FIRST tight the bleeder and THEN loose the pedal.
Keep doing that until NO air comes out of the system.
While you are doing this second stage keep filling up the reservoir and do not let the master cylinder **** air in.

SOURCE: Front brake master cylinder wont pump fluid

Yes, you can buy a master cylinder rebuild kit. If you can't find a rebuild kit the whole thing can also be replaced.

SOURCE: rear brakes lock up

The most likely problem will be the rubber line coming from the splitter leading to the caliper. With age these get soft inside allowing fluid to pass one way easily but not the other. Remove this line and blow through it both ways to insure the fluid can pass both ways. If needed check the line from the master cylinder to the splitter as well.