Your rough idle could be lack of fuel getting to a cyinder. Perhaps you have a "broken" injector that is not putting fuel in the intake but is just leaking it to the outside world. You may low fuel pressure too.
Have you read the codes? This culd be helpful but in your case I would correct the fuel leak before worrying about anything else.
I agree with 12Ounce and the coach. The fuel rail rail runs along the top of the valve covers. I would suspect a leak somewhere in the fuel system. I am not sure if a valve could even cause the problem. If you have a missing valve and valve stem the airflow woulf be from outside to inside and thus nothing should leak to the outside world.