Grant,
You can simply polish the edges of the glass with some fairly fine sand paper. Just run the sand paper back and forth from edge to edge until you're happy with the polish. If you don't, the glass will slowly wear away at the plastic tracks.
I would suggest just replacing the bottom piece of wood that the track sits on with a slightly taller piece to make the glass sit in the track properly. Otherwise you'll find that making that few millimetres worth count will be harder than you think!
Thanks,
Darren Hamill
http://www.hamillreptiles.com