The best way for me to get over my OCD on these things and really all projects is to call a thing "done" at some point. Off the rack it's usually after I've tested the truss rod and carefully inspected/set it up at home, on a parts a build it's when I'm satisfied that the finish is as far as I can or am willing to go (sometimes I'm shooting for perfect, sometimes a small imperfection makes that impossible relaxes me a bit). But once it's done and I call it, that's it. Time to stop worrying and start enjoying it for what it is.
For your own sanity I'd say once you get this fixed, just call it. I'm sure you didn't spend all that money on a nice guitar only for it to make you feel feel uncomfortable handling it.