Ditto to all the above, plus try a power balance test. Run the engine at a constant speed a little above idle (1000-1500 RPM) with a tachometer and a vacuum gauge attached. Pull one spark plug wire at a time and record the RPM and vacuum drop. A cylinder that's not pulling its share of the load will have little to no RPM or vacuum change. Good cylinders will make a noticeable change when the spark is disabled.

A stuck or burned valve is probably causing the rough running. Valve guides usually cause a puff of smoke from the exhaust after coasting and getting back on the gas, or on startup after sitting overnight.
Jerry

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