Oh my goodness! The same thing happened with my bun Myra when she was rescued!

I don’t have any direct experience but here are some links that may be useful:

http://www.bio.miami.edu/hare/surpriselitter.html

https://rabbit.org/care/babies.html

https://rabbit.org/care/newborn.html

http://www.mybunny.org/info/caring-for-newborn-baby-rabbits/

Most of us here don’t have experience with babies, but rabbitsonline.net has more ppl experienced with babies.

My understanding is you don’t clean the nest, the mom keeps it clean. Usually the mom licks the buns belly and that triggers them to poop and pee, so she just licks it up.

I think the other links I shared should answer some of your other questions (including about weaning etc.)!

At the rescue they started to handle babies daily to help them get used to it.

Since BinkyBunny prohibits discussion on intentional breeding, not many users have experience in kit care. There is great information on it here: https://wabbitwiki.com/wiki/Baby_rabbits_(domestic) , as well as here: https://flashsplace.webs.com/accidentallitters.htm  … below are responses based on my interpretation of information found in those links, not from my own experience with kit care. Please review prioritize reading both the links as reference, rather than my responses below:

1. It’s best to check sometime in the late morning/immediately after the mother typically feeds the rabbits (which only occurs 1-2 a day). Check for a nice belly on the babies and watch out for wrinkling, which is a sign of dehydration
2. The baby rabbits will naturally become somewhat independent and will begin grazing on pellets and hay around that you are feeding the mother. You do not need to worry about timing it yourself, as they will do it on their own — they are actually likely to start pretty soon.
3. Quoted in the second link I shared: “Days 10-14 – Clean the nest for the first time. It’s important when the babies open their eyes, to clean the nest to minimise the risk of conjunctivitis. It’s important to save as much of the nest as possible, especially the fur, so keep anything that is not soiled. Keeping as much of the nest as possible means that both mum and babies will know where the nest is and it will retain its smell.
   There is no set way to clean a nest, you just need to make it as stress free for mummy as possible. Sometimes having a spare shoe box made up into a nest can be useful to put the babies in whilst removing all the soiled nest material from the original nest. After the first time, you can clean the nest whenever you feel it needs it, always saving as much of the nest material as possible.” … as noted in the Wabbitwiki, if the kits are not urinating/defecating, you need to stimulate it to happen. Directions on how to do so are listed in the Wabbitwiki.
4. My (naive) understanding is that Jupiter should be eating her cecotropes — her milk is what’s going to help the kits develop. It is orphaned baby rabbits where there’s more discussion of getting rabbit cecotropes
5. Probably once they are nearly successfully weaned/much more independent. That’s my naive guess though.

If your bunnies aren’t that very active and thin, then I would recommend once they are three weeks old then you should start feeding the baby bunnies unlimited timothy alfalfa hay (I highly recommend Oxbow hay because I believe it has the most nutrients) and once your baby bunnies are 3-4 weeks old they should start being fed unlimited alfalfa pellets (until they are 6 months old, this age is when you should start feeding them adult rabbit pellets.)

This will help your baby bunnies consume a lot of nutrients. If your baby bunnies are already eating alfalfa hay and alfalfa pellets, maybe feed them more than usual? When a rabbit is thin it sometimes means he/she is not getting enough nutrients.

How are the babies and momma doing now?

Glad to hear they are doing well!

Sorry I had to remove the picture, on the forum we only allow baby pics if the poster will be keeping them (to discourage intentional breeding etc.), but once you have picked out the ones you are keeping we’d love to see pictures of them!