I understand what you are saying....it sounds like you are doing everything right.....and yes, you can make somekind of mark on the underside of the lace to mark the "middle".....I have a client that marks the back of her piece with a sharpie marker....it doesn't show from the other side . (she has a small piece with no crown and no tag, all lace....so sometimes determining front from back is a challenge).
so perhaps a very small marking with a sharpie right on the base will be a good trick for you. it really sounds like you have your act together and that you know what you are doing and what you want to achieve....and you may be right about needing to either shave a tiny bit more hair OR trimming the base down a bit.....with the stretch factor of the lace, to make it meet up exactly right. I think MB once said he actually makes his pieces 1/4" smaller than his bald area and then stretches to accomodate...giving a nice snug fit.
DebbieS.