What is causing Honda Civic rough idle?

My 2006 Honda Civic w/ 1.8l engine has a rough idle. I replaced the passenger motor mount and spark plugs, but no luck. When warm it idles around 550-600 rpm and will dip down to 500 or even lower. It feels like it is about to stall, but goes back up to 550-600, like a hiccup. I checked the air filter and it was clean. I cleaned the MAF sensor, but no measurable difference. The old spark plugs were a little dark (dry soot). Just noticed valve cover is leaking too. Car was sitting for a few months. No check engine light. My next move is to replace the valve cover gasket and clean the throttle body.

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