I usually drain the coolant, remove the thermostat and put the housing back on, fill with distilled water and your rad flush of choice, run it for a good 30 mins or more. Then I flush and re-fill about 2 times with distilled water, finishing with a 50/50 coolant mix and new thermotat. Don't forget to drain the block, there is a bolt for it. I also run a hose on the exiting heater core hose to reverse flush it for the bigger debris. That is my procedure for neglected cooling systems on cars that I buy.
