Start off with matching the left one to the right. The left is the one bothering you, so assume the angle of the right clipon is more optimal. Don't get too hung up on alignmenmt marks; there's no "right" setting. Different people like them at a different height and angle...if you can adjust something on the bike to make it more comfortable, then do it.
I have Cyclecats on my SS, which are adjustable not only for height and rotation around the fork tube, but angle as well. I used to obsess about making sure that each was the EXACT mirror of the other...I made templates, measured angles, even used a protractor!
These days, if I make a change, I just eyeball it, ride it, and adjust as necessary. Sometimes this adjustment may involve only one side! You'd never be able to tell if they were different just by looking---I can't---but I don't care if they are. I just find a position that I like and go with it.