If the engine is running roughly at idle, you may want to investigate the fuel system. These engines connonly have problems with rust accumulating in the fuel rail, restricting injector flow; if you remove the rail and look inside, it is uaually obvious. If you don't want to remove it, there are tools on the market to pulse the injectors while monitoring fuel pressure drop to check for flow restrictions.
Another possibility is an internal vacuum leak in the intake belly pan area. Disconnect the PCV air inlet on the left valve cover and plug the valce cover hole, or have someone hold their hand over it. Go to the other dside, disconnect the PCV valve from the valve cover, and check for suction at the valve cover. If you can feel any, or measure any with a vacuum gauge at teh hole, then the intake manifold must be removed to repair the leaking belly pan gasket. Often, if this leak is present, the engine will be experiencing some oil consumption or have some slight detonation also.
A dirty throttle body or idle air control are also possibilities; if the idle speed drops too low it may run roughly.
