I'm afraid I'm not sure on the exact procedure on EGR cleaning since my Pathfinder doesn't have an EGR system. I'd imagine you could take the valve off and spray it with brake cleaner and ensure the hoses aren't restricted either, maybe blow some compressed air through it - but since you've checked them all I doubt they would be restricted.
I suggested EGR because
page EC-267 of the factory service manual suggested it, among other things. It may be worth trying to follow the diagnosis procedure that begins on EC-268 as best as you can, as well.
Did you ensure the gap on the spark plugs was correct before installing? They should be within spec from the factory and the NGK plugs I used I didn't check and my Pathfinder has no problems, but it would not have hurt to double check.