Rust can only come from the water pump impeller, water pump shaft, cross-over tube, heater hose tubes, and the engine block. The water pump housing, thermostat housing, and heads are aluminum. The radiator and heater core are either aluminum or copper. In addition to a clogged radiator, it is possible for the impeller to separate from the shaft (no flow), or the fins of the impeller rust-off (reduced flow).
Running it as long as you did, with the various problems you described is not good.