Misfire on 2003 Lincoln LS

My 2003 LS V6 has been misfiring. I've had the codes read and it states coil #3. I have had a complete tune-up last week, replacing all coils, plugs, valves and gasket covers and even bought a brand new $150 battery. Check engine light is still one and it idles so low it cuts off and I have to restart it several times. It shakes violenty when stopped and if its in "P" park and press the accelator completely to the floor it does rev at all. I do smell a rich order "fumes" from the exhaust. I have spent $2,000 and Ford wants me to spend an additional $1,200 for a new computer "they think will fix it". Love my car but it has been in and out of the shop for the last month and this problem has been going on for almost a year. What's really going on???????

Asked by for the 2003 Lincoln LS
I had the same coil go bad. I replaced all of them at $50. a pop plus $7.00 for each spark plug. you can do it your self and it takes about 15 minutes is all. Make sure there is no oil on the spark plugs when you take them out. Oh, disconect the battery first before changing them, and then to clear the engine light you can go to Shucks or disconect the battery and it should clear.
We replaced all the coils and spark plugs ourselves and it took in in for the valves to be cleaned and other maintenance. After all of that same thing. We went forward with having the PCM replaced for $1,538 parts labor and etc. and have not had any other problems since.