The ignition timing should first be set with a timing light, after following the manufacturer's instructions about disabling the electronic advance while the timing is being adjusted. It is not adequate to set the timing statically, nor to set it at TDC if that is not the recommended setting. There should be an emission label on the underside of the hood, which contains the timing specification and instructions about disabling the advance. If that label is missing, you'll have to consult a service manual
I would also replace the fuel filter. If that doesn't clear up the problem, I suggest running a compression check. If any cylinder has compression that is below the minimum specification, or is more than 20 pounds below the compression of any other cylinder; the engine will not be able to be made to run without missing.
If the compression is good in all cylinders, I would remove and clean the EGR valve; and make sure it closes fully. I would also clean the sensor wire in the mass airflow sensor with electrical contact cleaner. In addition, I would clean the throttle body and remove and clean the idle air control valve, and make sure it operates freely.
There might be a vacuum hose leak; particularly at the MAP sensor or PCV valve; so check all the vacuum hoses, including the one that goes to the power brake booster. If any vacuum hoses are disconnected, or connected improperly, this can cause misfiring.
If the missing continues; I would reset the spark plug gap to .040".
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