Hi there,
             I have backlit two DMGs now and notice that the alignment of the screen through the screen glass is different on each gameboy. I noticed this before I even did the backlight mods. It is more noticeable once the bivert mod has been done as the position of the inverted dark borders can be seen.

Does anyone know a solution to this?

Maybe you could put a little piece of a toothpick or something between the glass and the plastic mounting frame to correct it somewhat.  Mine's a little off as well, but after a little while, it stopped bothering me.