Well, I've never done it, but I'd try 5 min epoxy rather than super glue. You can get stuff that dries crystal clear. You'd have to sand it smooth with the canopy and then use a polishing kit on the canopy to bring it back to clear.
Maybe someone on the list has an extra canopy they could send you? What manufacturer/scale is it?
Also might want to try www.squadron.com. They have all kinds of vac-form canaopies that may be a better bet than trying to repair the one you've got.
Good luck!
M.