i just bought the bike today but there is some kind of mod on the shifter it moved it up one hole dose anyone have help for me idk what to even do or if i can just move the peg back down one hole and put the passenger pegs back were they go
That appears to be a set of rearsets, definitely not stock. you can always try it out then see if it comfortable for you, I don't believe it will hurt anything.
I have a Banke shifter setup on my s3, with the stock location for the pegs, that was comfortable for me.