mmmm not sounding too good ..

If I understand the sequence of events ...
Frozen engine that you actualy started or a short period.
Once unfrozen you ran it on several occasions when it either got pretty hot or made "odd" noises from the plumbing.
Eventually diagnosed as waterpump sheared impeller - WP replaced
After pump replaced misfire attributed to a further water leak .. possibly HBV.
Now major noises from engine.
Possible scenario's:
... you possibly "cooked" the engine though "local boiling" when running it with no waterpump impellor, this has caused a headgasket failure
... Cam belt/tensioners got soaked/stressed and have now failed
... Parts of the old impellor remained in the system and have just met up with the new impellor