There commercial products available at paint stores for treating mold on wood. Household laundry products such as diluted chlorine bleach, or a solution of borax in water, will also kill mold spores and help to eliminate the dark color. You might also try one of the many non-chlorine bleaches available.

Oxalic acid has been used for years as a bleach to lighten wood color. I haven't tried it for killing off mold, but it would probably work, too.

Whatever you treat the wood with is going to need to be removed before glassing, so rinse it well and then rinse it some more. All that rinsing will raise the grain so you'll need to do some light sanding with a fine-grit sandpaper.

If bleaching and sanding don't remove the stains you ca look at the many stain colors available. Or glass it and use a tinted varnish over the glass.

If you have some areas with truly obnoxious discolorations consider covering those spots with decorative pieces of veneer. There are many designs available which are precut and ready to glue on. Once the glue hardens you sand down the edges and cover with the glass. It will look like a custom inlay.

Once you have the wood completely sealed in epoxy no water vapor can get in to allow any mold spores to continue growing. If you are ready to go with glassing you might just do a light sanding and if that removes theproblem then skip the bleach but put on the first coat or resin and glass.

Hope this helps
PGJ