help 02 cougar

is it possible that the egr could cause a miss on cyl1 and 3 only?

I'm not familiar with that year, so I don't know if it has a COP (Coil on plug). What I do in that type of situation is swap the 1 and 3 with the 2 and 4 spark plugs and COP's. Then see what happens after clearing the codes. If it comes back but on the 2 and 4, then it is a good bet those COP's are bad. Replace them and all new spark plugs. If it stays with 1 and 3, check the wires going to the COP's. Not familiar with what engine is in your car, but a bad EGR or one of the crappy designed intakes will foul the plugs closest to the EGR and require those plugs to be cleaned on a regular basis.