I have the exact same complaint about my 06 civic. After the engine
heats up it idles at around 600 rpms. I need to rev it alot to prevent
that clunking noise or stall it out. When its cold in idles around 1000
and I have no problems. Also, I heard a knocking noise coming from the
engine so I took it to the dealer. After leaving it over night they
told me that honda canada said to change the Block. Its possible that
the rod came loose in the crank case. Please keep me posted on what
happens with you car.