Is that really the valve clearance spec for that motor? Even though what you're describing sounds like you have them too loose (if it's the valves), that spec seems kindof tight to me. Maybe it's right. I dunno. My civic was .007-.009" intake, .009-.011" exhaust.

If the specs are correct, and you're sure it's valvetrain noisse, then it sounds like you may not have the feel of those feeler gauges down.