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I had this same issue last year when I changed my valve cover gasket. I tried all the suggestions I could find online and even changed spark plugs, ignition coils, new valve cover, etc. and it still ran like crap. I finally got fed up and decided I was going to drive it to work regardless. After driving about 5 miles, the engine smoothed out and ran perfect after that. The only explanation I found that made sense to me was related to the oxygen sensors. Prior to changing the valve cover gasket, the electronics had adjusted to accommodate the vacuum leak as best it could. When the leak was fixed, the setting were incorrect for the new condition. Even though the oxygen sensors are "heated" they still need to get to at least 600 degrees. Up to the point where I drove it to work, I had never gave it a chance to adjust to the new readings. Some will tell you that the sensors are ready right away but that is not necessarily the case. You can check by removing one and checking the temp. Also, even if the sensor is ready quickly, the system take a number of readings before it resets. I'm not sure how long that takes but its worth giving it a try to see if the engine smooths out.
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