Luckily the Citadel DLC is next up in my trilogy playthrough so I should get the chance to fix it soon.
I can't say that I've had the transparent hair thing, but one thing about my Shep's hair that annoys me is one random strand that appears to be not connected to her head! I use Kelly's ME3 hair mesh as part of a custom headmorph but I must have changed one of the values somewhere as the same random strand isn't there on Kelly. I really should just load it up in gibbed and play around with it, but it's such a small thing that I can't be bothered! it just irritates me when I see it!