Step 1: Drain all fluid from cooling system. (best done when cold)
Step 2: Fill system with DISTILLED water + a cooling system flush kit or CLR (CLR tends to be cheaper)
Step 3: Set heater controls to max heat
Step 4: Start truck and allow to reach operating temperature. Let run for an additional 15 minutes.
Step 5: Allow engine to cool down, usually takes 3-4 hours.
Step 6: Drain cooling system by pulling lower radiator hose. (this allows large particulate matter to be evacuated from the system, whereas the petcock may get plugged)
Step 7: Back-flush the heater core by disconnecting the heater hoses and hooking them up to your garden hose- alternate direction of flow until you get clear water coming from both directions.
Step 8: Now is a good time to inspect/replace your thermostat
Step 9: Reconnect all hoses
Step 10: Fill cooling system to required levels, using either the 50/50 pre-mix, or by using straight coolant and distilled water.
Following the above procedure should take about half a day, mainly because you need to wait for the engine to cool back down once you've put the cooling system flush (or CLR) into the system. Shouldn't have any further problems with discolored coolant.
FYI: This may not be rust at all, but "Radiator Stop Leak". If you aren't familiar with this vehicle's previous service history, this stuff may have been used. I personally HATE the crap, as all it does (IMO) is to hide (temporarily) a real problem, and tends to clog the tiny cooling passages of the engine, heater core and radiator, leading to poor cooling system circulation & poor heater performance. All around bad stuff, and it is notoriously difficult to remove from the system. Can usually tell by the rust-colored buildup at the radiator fill neck; looks like rust, but when rubbed between two fingers, crushes to super-fine particles, with almost a grease-like feel.
FYI2: Aside from flushing the heater core, avoid using tap water for your cooling system. The minerals in it tends to create a galvanic reaction, leading to premature failure of aluminum components. To be sure, in an emergency situation, I'd use tap water, but only then- distilled water has had all the minerals removed, and thereby reduces the corrosion caused by galvanic reaction.