Is the ECU putting out any codes? could be many things but irregular idle is usually AFM, or air leak related.
Rusty water is common enough. Just a build up of scale in the cooling system from lack of servicing.
If you want to get rid of most of it, Drain the cooling system, Take off the thermostat housing at the bottom of the engine as well as the top and bottom rad hose.
Put your garden hose in the top tank and run it until the water coming out the bottom is clear then do the same with the rad.
Put it all back together and refill with fresh coolant. Should flush most of it out, you would have loosened it with your previous flush.