I don't know how to get them out individually, or how to stop them.  In my experience waxworms leave behind a trail of webbing as they eat through things, so maybe due to their shear number it's turned into something bigger this time.  Can you get the whole thing out of the container; worms, feed, webbing and all?  Then you could set the entire mess on top of the new substrate and they should move down where there's more food, especially if you could peel off some of the webbing or maybe split the whole mess into 2 chunks so you could have some exposure to the new food that isn't cut off by webbing .  After most of them move you could remove the mess off the new feed and hopefully have new feed and worms left behind.  It might be difficult to get the whole mess out without crushing worms depending on how your set-up is, but I'd imagine you could do it without losing too many.  Congratulations though on getting them this far!  You could write a book once you get all the details worked out, a sort of trouble-shooting guide  : ).