1. I shoot with three vanes with the cock vane down not out.
Look into the end of the receiver that you will place your arrow nock into and verify that the "V" of the internal locator is vertical
Lost me here. No "V" seen just a vertical bar. Only "V" is at the other end of the guide. So the middle indentation is showing the correct position of the cock vane.
I always mark the receiver with a paint mark in the center indentation of the receiver
Are you saying that you mark the center hole?
2. Adjustment of the shaft rest.
I set the V shaft rest at the top of the fletcher slightly to the left when viewed from the back, nock side of the fletcher
Is this for right or left helical? the "V" cannot be moved to the top it is fixed with a screw and the adjustment would be right,center, or left. No marks to go by so you could be far left or adjust from left to any point to center and the same for the right.
3. Yes, and thanks for the photos