if you have a cylinder 6 misfire, it can still be the EGR ports. If you pull the upper intake, you'll have ports to each cylinder for the egr, they are about the size of a dime with a small hole in the center. If they are all clogged except 6, you'll get excessive flow and a miss, especially at cold start up.
PS the way you check to see if you have the updated bank 2 valve cover is pull off the PCV hose on the left of the valve cover (left as you are facing the front of the car and the valve cover) and look inside. The updated ones have a small breather hole. No hole, no update.