2000 Ford Taurus Changing the coil on a 6 cyl. 24 valves DO

I have a Ford Taurus 2000 with the Duratec engine 24 valves DOHC.Lately, the engine has misfired following many rainy days and a coil situated in front of the car (grill side) was changed.Following that change, after driving about 20 miles, the engine started to misfire again and the following day the misfiring was more serious and the emission control light turn itself on again. Days later, I return to the garage, he connected his electronic device and came up with a diagnostic that the cylinder no 3 had a problem, probably the coil but he is not 100% sure. The cylinder no 3 being on the passenger side of the engine (almost under the windshield), he tells me there is not much space to get a coil in place unless the ''upper intake'' is taken off from the top of the engine. Is the diagnostic good. and is it necessary the take off the upper intake (the black cover on top of the engine,) ? Motorcraft spark plugs changed, only 7042 miles on them. Thanks very much for you advice.