Well, technically speaking, the looser your nock/string fit, the better your arrow flight should be. Any form of interference on the arrow will affect flight. The less interference, the better.
As to unevenly sanding your nocks, it shouldn't make any difference (well, not enough for you to notice)
Looking at your setup, I'd say that your shfts are way too stiff. At 25", you're only pulling in the region of 30-32# If it were me, I would've left the arrows full length. You could try adding extra weight up front (try 200-250gn) but adding weight to skinny carbons doesn't affect the dynamic spine as much as changing their length.