>what more do i need to do
I'd reduce them down to just the frames they can cover. If that requires building a smaller box, then that's what I'd do.
>what do i do with the frames that have been chewed up? do i cut off what i can and boil it down?
First, I would cut out all the baddly webbed parts and leave the rest for the bees to fix. If the whole comb is webbed, then cut the whole thing out.