Re: Advice on taking off supers
It sounds like you certainly have an interesting set up. Shallows aren't really popular for bottom brood chambers. Also, your post seems to suggest that you left the queen excluder on all winter. This is a big no no. The queen has to be able to move with the cluster during the cold months or they will never move on to higher stores (could be why your surviving numbers are small). If your colony population is low then just remove one medium of your capped honey and don't replace it with anything for now. Empty comb isn't going to do them any good until their numbers recover.
...This, and my heart, and all the Bees
Which in the Clover dwell.