Wish I had more time, but briefly, if the clutch is going, the pilot or throwout bearing can make noise, typically as you are clutching, but some load situations when you pop out of gear, etc...and add that the friction plates can also make noise when under load, etc.

The alternator symptoms are related to the battery going dead/weak even though you were running the engine, etc. You can measure the charge with a meter as it runs...if the engine running isn't adding juice on your reading, you're in trouble.

The exhaust is your main clue on the manifold, with the engine running, block the exhaust with a rag, etc, and see if the ticking or whatever under there, gets louder/changes in character, etc.