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I have a 2000 5.4L. Yesterday while driving, the motor just started running rough. Thought it might be water in the fuel so I put in some dryer, filled the tank, but still did not solve the problem. The check engine light is both flashing and staying on. If I drive it over 40mph it really shakes and vibrates. My oil and tranny fluid are both clean, no signs of water in them. No other problems other than it running very rough. Has anyone had this problem before??
Like Alfred said you'll need to get it scanned and see what trouble code turned the check engine light on. Most likely you just have a bad spark plug or COP (Coil On Plug).
Some parts stores such as Autozone will scan it for you for free. Just don't let them talk you into buying a bunch of parts without some more diagnosis though. If you post the trouble code here, not just the description of it, we should be able to help you with it.