Flush it. Old water in a system will look exactly like what you speak of, a nasty brown mess. My wifes Taurus was that way as was another car I had some time ago.
Don't be surprised if you have to flush it a couple of times, and be sure to use an additive and follow the instructions!!
I had to do it 3 times once. And still the water didn't look real "clean". What can happen is that the crap will restrict the flow of water throughout the system and cause it to overheat, its happend to me. It can also clog your heater core and then you wont have a heater.
So, in short, flush it a couple of times and see what happens. Let us know how it goes!
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2001 Mustang "Mach 1" SVO siamesed 351 stroked to 417ci,Yates heads, solid roller,Trans King glide.
Best 1/4 ET 9.17 (ALL MOTOR)
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