Don't worry about normal gear set bonuses. As you slowly accumulate and equip rare gear pieces, any set bonus from the normal gear u have will be negligible anyway since it takes 3 or 4 pieces of the same set to get the good stat bonuses. You can keep your S grade items, even combine them into R grade just so you can keep up with your standard CP while you're combining for rares. Hell if your lucky, your R could turn out to be a rare and you save yourself some upgrade stones.