Trouble with my KTM brakes

Replace the fluid front and rear and bleed. You do this at the same time BTW - Don't drain the fluid per se, just run lots of fresh fluid thru the system. A miti-vac makes this easier but is still better done with two people. Also level up the front master cylinder before starting; put the bike on a stand, lock the bars at full lock with a tiedown, then level up the cylinder by rotating the assembly on the bar.

Also check your pads. A single mud ride can chew up a set of rear pads no problem.

My brakes get bled 3-4 times a year. When you replace the rear pads, pushing the piston in to fit the new pads will usually backwash dirty fluid into the reservoir. Watch the clear reservoir as you push the piston in. Yucky stuff will probably back up into it.

This will give you a good start, but the '00 and '01 front master cylinders seem to be problematic based on posts seen here.

Dirt bike brakes unfortunately need maintenance BEFORE they start to show symptoms of problems. By then you probably have contaminated fluid grating on your master and slave cylinder pistons.