coolant is bubbling. knocking sound from engine?

Both these problems began after the the thermostat on my renault megane '04 burst a seal and the engine overheated due to it running dry.
The thermostat has been replaced and there is no longer a leak.
At the coolant expansion bottle the coolant appears to be bubbling and there is a smell of exhaust gas. Could this be caused by cracked head gasket? And would replacing this solve the problem or is there likely to be damage to the cooling lines?
The knocking noise, i have been told is most likely a big end bearing. However i have removed the sump and inspected all four bearings and found no signs of wear or damage other than some very slight discolouring on one bearing. However what i did find was the anti-emulsion mat had 'shrivelled', become brittle and wrapped itself around the bottom of the oil pump. (the opening to the pump was unobstructed). I have also turned the engine using the crankshaft pulley and there appears to be nothing impeding it's revolution. The only thing is that turning becomes a little stiff when the cylinders pass each other at the same height, which would make sense to me to be perfectly normal. Is it possible that the knocking noise was simply due to anti-emulsion mat? And is it worth replacing the bearing shells while i'm there?
I be grateful for any thoughts.

Nicky
December 2009