Uh Oh !! Bad knocking !!

If it were me, I'd pull it out, and carefully disassemble and inspect it. If it runs different and makes noise, you broke something. Running it more will not make the repairs any less. Pull it. Give it an autopsy.

I will never, ever, run a new bearing on an old journal without first measuring it it carefully for taper and size. And no, plastigage will not be good enough.