2005 Honda Civic Hybrid Engine noise

The trouble codes you have are all relating to an engine misfire. My concern is that the sound goes away when you remove power to the #2 coil. Have you removed the spark plug to inspect it?

Yes I remove spark plugs I actually changed them all the ones in cylinder 1 and 2 had carbon deposits on them cylinder 3 and 4 were normal looking I don't know if you know this but theirs 2 spark plugs per cylinder

Hi again:

yes, I'm familiar with the design. Listen, if you clear the trouble codes, do the same ones come back? Also, have you checked compression in the #2 cylinder? I question a burnt valve.

I have not done compression check, I'm not sure on the procedure for compression check on hybrid, someone told me I need a special machine. Do you know if this is true?

It's still an internal combustion engine. Here are directions.

https://www.2carpros.com/articles/how-to-test-engine-compression