If im right in thinking its a 4 cylinder, pinpoint the problem cylinders thus: -
From stone cold, start the engine and feel all the exhaust header pipes, the ones that stay cold are the problem...Take it from there.
You say it will run with the outside plugs removed, you should not do this unless the plugs are in the HT caps and they are grounded, it can damage your electronic ignition, just something i once read...no personal experience of this