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The orange colored stuff is a result of moisture in the brake system. The ethers that make up the corrossion inhibitors have absorbed the moisture and have now turned to the orange color that you see. Rust will sink. It is heavier than the fluid as it isstill a metal. There is no carbon steel in your master cylinder, therefore it is not rust.
The orange color is a result of a chemical reaction not resulting from the metal but from the H2O. It is a designed process of degradation, so don't worry too much.
DOT 3, 4 and 5.1 brake fluid are all glycol-based fluids and designed to operate with a certain amount acceptable moisture with limit. The "DOT SAE" classification of 3, 4 or 5.1 determines the available temperature range and moisture limits.
"DOT 5" is a silicone based fluid and has no moisture classification because silicone does not absorb moisture. There is no moisture limit in a DOT 5 silicone brake system.Dot 5 systems, or silicone brake fluid systems, use the same associated metal parts as used in glycol systems but use different rubber compounds in their various parts such as seals and hoses that do not allow for moisture absorption as easily as the 3, 4 and 5.1 brake systems do.
DOT 3, 4 and 5.1 are hygroscopic as mentioned earlier and disperse moisture throughout the brake fluid. This is why completely flushing the old fluid out is required for maintenance with glycol systems. The H2O is always present at some level because there is always some level detectable in the rubber. The "moisture" will enter the system through the rubber. Know this and expect it. Your owners manual gives a service schedule of some order for its replacement because of it.
DOT 5 silicone fluid is hydrophobic, meaning it does not absorb H2O and will not dispurse it throughout the fluid. The "moisture" will sit on top of the fluid and remain there until removed. DOT 5 fluid usually has no maintenance interval because of the inabillity to introduce H2O into the system.
We cannot mix the two fluids. Once DOT 3, 4 or 5.1 has been used in a brake system, as mentioned there is always a certain amount of "moisture" present. DOT 5 will have reduced performance when H2O is introduced as the compressibillity of water is farhigher than that of brake fluid.
So, it ain't rust and it's normal for what you're seeing if the fluid has not been flushed-out in quite a while. Unfortunately the orange you are seeing is throughout the fluids lines and passages and you're stuck with a good portion of it as a result. Don't worry about it though and just do what you can. Use a toothbrush and scrub the masters reservoir clear of it and flush half a big bottle of it through until runs clear on bothe calipers. Run a clear tube from the bleeder screw at one caliper to a soupcan on the floor and with the master cylinder top off keep filling the reservoir full as you pump the lever to pass the fluid through that caliper. Then do the other side. Keep filling and pumping the lever until the fluid runs clear. Don't worry about pressure bleeding, meaning holding the lever and closing the bleeder then pumping-up the lever again, just keep the reservoir full and pump 'til it's clear. Do it to both calipers and as long as you do not let the reservoir run dry (introducing air) then just close the bleeder screws when you're done. Piece-O-Cake.
Do it again next year, maybe the year after if you're the lazy type, but don't forget to do it in a year or two from now, preferable over the Winter when you've nothing else to do.
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