Well, to come in and offer some help to this lets start with eliminating the obvious. You asked if it could be a head gasket. Yes and no. Yes it could be a head gasket as that will cause a misfire on a cylinder if you are low on compression. No I highly doubt your 01 GT has a head gasket issue since the passenger side of the engine bay is straight in order cylinders from front to back are 1,2,3,4. Drivers side are 5,6,7,8. So if it were in a fact a head gasket you would need both sides as your codes are for the rear on one bank and front on another bank. When you pulled the plugs out did they look bad? Was they soaked with gas? If this car is stock buy yourself 8 new spark plugs (Motorcraft if it is stock) a nice good copper plug will work if it is modded. Also pick up 2 new coils and change out the right side rear coil and drivers side front coil and repost your findings. I bet cylinders 4 and 5 arent missing anymore after that. Let us know.