I just got done rebuilding an 1989 Big Boss 4x6 250 and had the same problem. The brakes came in a box and the fluid inside was like sludge. I also found that most of the bleed valve were trash. I did pull the master cylider apart and clean it. I did not replace any parts since it all looked OK. I started by removing the bleed valve and flushing clean fluid through the lines by pumping the brake. After it came out clean, I put the bleed valve back and used a suction style bleeder to remove the air. I never pulled the caliper apart, but I did grease the slides on the other calipers.
The brake now work well. If I found a cheap rebuild kit, I would most likely rebuild them, but the money was spend elsewhere on the ATV.
I would go through the entire brake system. Important to be able to stop.....
A bad master cylinder would leak or not pump fluid. Make sure the inside is clean, fill with clean fluid, open a bleed valve, and see if pumping moves fluid.