Q: Engine shaking and knocking after spark plug replacement.

This sounds to me like the cylinder head has been severely damaged. If the burn of the coil and spark plug started on the plug end this would mean that combustion chamber temperatures from inside the engine were allowed past the electrode surface of the spark plug. The explosions from the fuel being ignited inside the engine must have caused the spark plug to burn up. I would first recommend having a qualified engine technician come and do an inspection of your engine. You may have a crack in your cylinder head. As for the knocking sound, a piece of metal from the cylinder head may have broken off during the rethreading process and fallen on to the piston. When the engine was started again the piece of metal must have been getting smashed between the valves and the piston itself. I would not run the engine anymore until the inspection is done to prevent any further damage.