This is how I fill my cooling system, haven't had a problem.
Remove the bungs in top of radiator and thermostat housing, turn the heater controls up to hottest setting.
Fill radiator through the bung hole, as soon as it is full, fit bung, continue filling through bung hole in thermo housing, as soon as full fit bung. make sure water bottle cap is on before driving.
Take for a drive till temp gauge shows normal and heat coming from heater, drive home and park and don't touch overnight.
Next day water level in bottle should be at correct level, too high, siphon some out, too low add, works for me and is how it says to do it in the workshop manual, good luck.
As for the noise it is hard to tell, remove the drive belt and spin pulleys and tensioners by hand, feel for roughness and listen for rumble. How long was the water pump dry for during head work, have you used Coolant? Could also be the fan bearing in the Timing cover, see how to fix on Forum, Regards Frank.



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