What were your modification?
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For the rabbits, I left the height roughly the same, but replaced the bottom with wire. Replaced the long sides with about 75% wire. Leaving them with a small 2x2 (roughly) space to go into that is completely closed in from the wind. I also added a run of wire length wise down the middle to create a male/female side. With that, I added doors on each side so the male and female side could be accessed separately.
For the ducks, of course I brought it much closer to the ground, replaced the half of one side with wire, just because the ducks don't mind the weather and changed the size of the nest boxes. The ducks don't use the roosts, so was able to save a little time/energy there as well.
I use deep litter in the chicken coop and it is working great with this coop. I'm experimenting with the ducks, but it's a different ballgame with all the water...