I figured it out with a friend last night. Turns out to be my water pump going bad.

 

Are you sure its the water pump? They rarely go bad on these cars. It does sound like a belt driven accessory though. Did you rule out the serp belt tensioner pully and idler pully? Those are quite common to eventually develop bad bearings.

Tip, you can replace just the bearings, instead of the whole pully. There are threads with standard bearing part number, which you can get anywhere, including Amazon.

 

I figured it was the water pump so I took the chance and bought a new OEM unit from honda and replaced it. Sound has went away so that's covered. Unfortunately I still can't figure out the vibration/rattle from the original post. Headers look fine, engine mounts are good too I think.