Your mechanic was 99% of the way there with the spark plugs out so a compression check should have been run to verify things are fine mechanically; and especially so considering that TSB about valve rotation.
Low compression can cause a misfire due to incomplete combustion so maybe the clicking sound is a spark jumping from the plug boot to the cylinder head.
Exhaust valves not rotating enough on their seats can have a tendency to burn also which leads to lowered compression which leads to misfires which leads to…
It’s a vicious cycle.