I' m not going to get into the " why' s" of a new string and replacing a loop based on the old one.

1. I eyeball the arrow in relationship to the flat part of the riser cutout and tweak it a little nock high. Then paper tune.
2. You may be able to twist the loop up and down the string just like a nut on a bolt. Twisting and pushing at the same time usually moves it in the direction you want. I recommend having the loop pointing directly behind the string. Reason: when I' ve tried to leave the loop a partial turn pointing right or left to make the peep line up, it has effected arrow flight before. It made a whipping motion I guess upon release.
3. No. It has to be one way or the other. You can' t test one way and then make changes and expect it to fly the same. (If read and meant what you posted)
4. Can' t define what your " small" means, but yes it can make a difference. Especially with broadheads.
Big bulls types faster than I do!