what's the best way to clean brown fluid with possibly gunk in the master cylinder, can you flush it using the spout on the brake caliper?

Suck the old brake fluid out of the reservoir using a turkey baster of equivalent, then refill it with new fluid. Starting at the front left, work your way around the car bleeding the brakes until you get nothing but fresh, clean fluid from each bleeder valve.

You might consider replacing all of the brake lines though, as they are prone to rust through when the fluid gets as bad as you describe. All those rust particles gotta come from somewhere, and that's usually the inside of the brake line.

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Used to own:
'82 Dodge D150
Erson 270 Cam, O/S valves, mild port work, ~9.5:1 compression

Currently fighting with an '85 VW Cabriolet

My other passion