Mice/New mouse had pups
I got a mouse off of Craigslist. Apparently she was a rescue (what I was told) and not much is known about her history. A week after I got her, she wound up giving birth to a litter of pups. After too many hours researching the care of a nursing doe, And suggestions from fancy breeders I'm sure I know what I need to about fancy does. My problem is that with all of this research came my doubts that my mouse is in fact fancy/domestic. Her personality fits to more of a house mouse from the wild than a tame domestic mouse. Because of this, I am now really hesitant of handling the pups at the recommended 3 days old.
Since I don't know for sure if she's wild or crossbred and how long she's been in captivity, I don't think it's humane to limit contact and release her and the pups into the wild, even with the suspicion that she is at least crossbred if not a second plus generation wild mouse. I would like for the pups to be as take as possible. What are the chances of her culling her litter if I do handle them after putting her in another cage with some yummy treats? Is it best to just wait until they are older since there are so many unknowns? I would hate to see her cull the litter due to my mistake :(
While a big part of that wild nature does indeed come from genetics, some if it can also be learned. If she wasn't handled as a pup, as most pet store mice aren't, she could still be very antisocial, skittish, and "wild," even if she came from a pet shop. This is even more common in shops that sell mice primarily as feeders for reptiles, where handling just isn't necessary. Between being a second generation and having you for a pet owner, the pups definitely have an excellent shot at being much more tame. If not - limiting contact won't help them remain wild or anything - they will have those instincts in full swing and be able to pick up at any point. I would give it a shot, but like you mentioned, this depends hugely on mom's behavior.
The pups will benefit from ANY early handling, and each day that goes by in their aging gives a better chance at survival exponentially, so do not be too concerned about rushing into it. Three days is great for really calm mothers with happy litters, but not required by any means to get nice mice. Usually by the time they have fur in, but their eyes aren't quite open, mom is becoming more comfortable with the situation, they will have their own smells (and be less subject to your scent), and they will still be docile enough to get in lots of handling. A good technique to try, should mom allow it, is to wash your hands first, touch a little of the litter (the cleaner stuff, obviously), and pick mom up once she is away from the nest. Contacting her, even a little, helps get her scent on your hands, and just like you mentioned already, separating her from the nest visually IF she isn't freaking out will be easier on her than watching you pick up each of her pups. You can also provide a treat on her return from the cage so she isn't immediately examining the pups, although many avid mommas will anyways.
The most important thing of all is to watch how mom behaves around the pups! Does she run to the nest when she sees you? Is she always in the nest? Does she leave them alone a lot, and explore treats when you offer them? If you "spot clean" the other areas of the cage (the nest does not need cleaned at all until they leave it on their own), does she become anxious, chasing you away, distracting you from the nest, or covering up her babies? Or does she just kind of check out what you're doing and move on? Any big signs of anxiety are red flags that both the behavior in question and any potential handling need to stop. Never pull her from the nest - she will have to be relaxed enough to be away from the nest and able to calmly be removed before any handling can take place. Health is just so much more important than the extra points in taming when it comes to new babies.
If anything goes wrong at a further on point, such as if you start handling them around a week instead of three days, you will be able to immediately stop any emergencies that occur when you return her, and will have a much better shot of handfeeding survivors at 7 or so days old than 3 days old. Obviously we don't want anything bad to happen in the first place, but first time moms are often unpredictable, and it's best to have a backup plan. Remember that around 2-3 weeks they may hit that "popcorn" stage regardless of how well they've been handled or tamed, so be careful with the little guys! :)
Congratulations on the (surprise!) litter! If there is anything else I can assist with, just ask, but I think you are pretty much on the right track already. :)