Mary Ann's comment sparked my memory and i went through your old posts and found this one from Mon Oct 21, 2013 on this thread -
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beckyhuff314":2b781vzt said:
All of my ND rabbits are pooping those same poops. They are like 4 times the regular poop size and long, not round. They look like mini dog poops. and smell just as bad. None of my rabbits are sick in any other way that i can tell. All are eating and drinking fine. This started last week for me. Wish I knew what was doing this as well.
And here you're rabbits are having intestinal issues as well -
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it is likely your adults got over the diseases and are non symptomatic carriers but the kits with their delicate digestive systems can not beat the disease and I believe it is the same disease you've had since early October.
I would do an intense sanitation of all the cages, bowls, waters, food scoops toys, just everything that was around the rabbits since October and isolate/quarantine any pregnant/nursing does and their kits until the kits are 8 weeks old.
However, the adults might re-infect the kits so you will just have to breed for resistance with the survivors.