Update. I built the shelf up a few mm with moleskin and a toothpick as a very slight retainer on the outer edge of the shelf. That took care of the knuckle cutting issue. Not sure if it is due to the height of the shelf, which isn't a whole lot, or the retainer, but I didn't hit my knuckle. Let's call that progress.
Now, bareshaft testing GT 500's full length and Easton 2018's at 30.25". They are shooting well right, which is a weak arrow. So, I looked at GT spine chart and it says I should be shooting .400 deflection. So, perhaps I was getting a super weak arrow flexing and hitting my hand. Likely compounded with a nock point too high or low. To confirm this I short drawed the bow and zip, right down the pike, the bare shafts flew perfectly straight.
So, I'm going to a friend's tonight to trim some of the weak arrows and try to get them stiff enough. Here's to hoping it works!!!