Engine shakes heavily during shut down

When i start my 136k miles 2010 Prius, it starts fine but i can hear a continuous low volume knocking.
After working for about 20minutes switching between Hybrid and Combustion Engine a couple of times, it switches to combustion, increases the rpm and doesn't switch back to Hybrid.
Coolant temperature would increase to 90-95 degree celsius and i see it boiling in the coolant tank.
When i off the car, the combustion engine shakes heavily.

Cylinder 3 and 4 misfire code come up sometimes.

CONS:
Car at 136000miles, Head gasket not yet changed.
Changed EGR valve
Changed Fuel injectors
Cleaned egr cooler and intake manifold.

PROS:
I am not losing coolant.

Checked cylinder valve via Borescope camera through spark plug hole and can see exhaust valves with heavy brownish build up.
Engine cylinders has some burn/rust looking surface and like an oil in Cylinder 4. (see attached pictures)

I want to know if this issue can be caused by a failed head gasket and if the cylinder build up is from same or something else.