Superfat or no superfat -- that's purely your choice. With zero superfat, the KOH weight is a bit higher yet than what I calculated. Excess unsaponfied fat will result in cloudy soap and separation. There are other reasons why liquid soap can be cloudy or separate, but excess fat is most likely the reason in your case. Yes, you can keep skimming it off -- it's just excess fat.
Six to 12 hours of cooking is waaaay overkill. I know this is the "way it's done" but it's not the way it has to be. You don't even need to cook at all especially since you're using glycerin -- a cold process method works fine.
But if you do cook, cook only long enough so the soap is zap free. That's usually under 1 hour, and often more like 1/2 hour. All you're doing by cooking longer is evaporating water out of the paste and consuming energy and time.