i would not remove take the thermostat out and run the car for a few days, sounds like a good way to make things worse.

Just pull the lower rad hose, to drain the coolant. Fill it back up through the LIM with water, put thermo back in
, then run the car till it opens to cycle the water for like 5-10min, then keep doing that untill the water is clear.

Then on the last one, fill the rad and LIM with coolant, any kind, green or yellow, dont matter. put new thermostat in, then run the car up to temp, with the the bleed screw ontop of the thermo housing open about 1-2 turns, wait for all the air bubbbles to come out and just solid coolant stream, it might take a while to completely get the air out.