I have a thread tie in place of your brass nock - IIAC you need at least one nock point with a D loop and where yours is is the latest trend - oops best practise. If you do without a nock point you'll most likely get creepage of your D loup - and you wouldn't be able to tell by how much either
Moving your peep a little up the string won't make much difference to your sight marks as its the distance your peep is from the arrow that counts (and roughly equates as you rightly surmise to anchor to eye distance. So its more important to set your peep to see through it at anchor.
Where does your arrow lie in relation to the "botton" hole - does it pass through level or is it below? If you have it significantly below it it eats up sight bar - though it is recommended to have it a little below so nearer the pivot point. I'm sure there are some "what height should my rest be?" threads on here.