what a mess you have there. Have you considered cabelas item #IG-119597 to hold your lures and flies.
these things are really good you can put two set-ups on every yellow insert,making one box have 36 different lures. you can also different leghts of leader on them 12" 24" 36" etc. so when you go to change lures you don't have to waste any fishing time.although you have to take some time to set them all up I think you'll find it worth while. They work great.