I would try to bleach a small section of the stains to see what happens.
If you use super glue, get a liquid type that is specifically meant for use on wood. Some formulations don't work as well on wood. Woodcraft sell several types.
Get this kit so you can inject the glue in the pocket. You might need to use a sharp knife to slice into through the lifted ply so you can get the glue in there. Once clamped and sanded the slice should disapear.
http://www.highlandwoodworking.com/cagluedispensepak.aspx
use some wax paper over the repair area when you clamp it to prevent the clamp from getting glued to the shell.