I was going to suggest you add the second nock point but see you already took care of that.
My other suggestion would have been to start your tuning with a very high nock point, one high enough that you know you will only have to go down. You might have been in a situation where your nock point was actually too low, resulting in just enough contact to correct your bare shaft and enough contact to give you wear on you rest from fletched arrows.
Ideally bare shafts should group right on top of fletched, but a little low and nock high in the target may offer a bit of forgiveness and improved rest clearance. I've come to like my bare shafts trending just slightly lower than my fletched shafts. It's not really noticeable at 20 yards but can be seen at 30.
That's something else...when in doubt with bare shafts, move back.