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Final update......it was the gasket between the intake manifold and the cylinder head. I took it to my dealer and they fixed it under warrenty.

On a side note the car was not loosing coolant. My fiance to the car to a jiffy lube last week for an oil change and the recipt said they checked the coolant and it was good. As such, when I found it empty panic set in. The tech at the dealer thinks Jiffy lube was lazy and didn't even check. It held a full reservoir for 3 days before the repair and one day after.

So if any one else has and very very rough idle and a misfire this may be your solution after you have checked the plugs, wires etc. Also my car is an 03 so TSB18-024-04 didn't apply like it may in other cases.