The Nissan Path

so recently I went about the duty of replacing rod bearings on a 2010 Nissan Pathfinder (4.0L V6) and finished, however though, it is not running correctly, it is pulling many misfire codes but after changing all the plugs and testing again it has not solved anything, I believe it may be the coils next but a bogging sound coming from the right side of the car makes me think there may be a clogged CAT but yet it is not pulling any codes for that. This problem is confusing me and I would really like to fix it before the winter comes and heavy snow...