That's a daunting task! Wait for warm day and get an experienced beek to help as you've got to find the Q in that lot and will definitely need support - if not just to have another pair of eyes!
I've never faced this before but at a guess she'll be with a brood area centred in the top brood box and first super. You'l need a couple of spare supers to put the boxes on as you take them off.
My suggestion is to re-assemble the hive with any super containing brood on the floor, then the brood box with brood, then the other bb, then an excluder with the broodless super on top.
imho after a few weeks the bottom super will be brood free and can be removed.
This advice may be rubbish and hopefully someone with more expertise will post .....
Good luck!
richard