Jeep 4.0 engine ticking noise after shut down

Jeep Wrangler ticking noise. The ticking appears every time after rotating the engine - no matter if that is done by running it or rotating from the crankshaft with ratchet. I can feel the ticking in the valve springs. Ticking is faster when engine is hot. I started to investigate the whole thing because engine does not run properly and computer is reporting misfire in cylinder #6. I just changed the spark plugs and oils, switched #1 and #6 fuel injectors, checked the cylinder compression and checked fuel injectors and spark plugs are working properly by looking with bare eye. The new spark plug #6 was all black after 20 km driving and 30 minutes of idling. What's the issue here with the 1) ticking and 2) running problem? It is possible they are not related. Please try to ignore the alternator bearing whining.