Congrats on the puppy, some of the crying is probably how young she is to be away from mom and litter mates, so it is great that you have a second dog. I'm also not saying it is always a bad thing if they are away from mom young, sometimes that is the best or only option. If your lab is on the verge of liking her I don't think I would force them to stay in the same kennel at night, since she won't be able to get away from the puppy if she chooses. You can try a stuffed toy with her or a t-shirt that smell likes you or another family member. That may make her more comfortable in her crate at night. We ended up with a 4 week old kitten and I have her a dog toy that was about 3 times her size, so she had something to cuddle up to at night (she was about a quarter of a pound when we got her). She is 4 now and carries the toy around with her sometimes and will alternate attacking and loving on it.
There are some toys for young animals that sound like they have a heart beat in them and can soothe some. I would be careful letting her out if she is crying, but doesn't need anything, they learn quickly that whinning will open the kennel door. It is hard I know. It sounds like she is adjusting since she is crying less and 5 minutes really isn't that long, especially if she is then quiet the rest of the night. Another thing you can try is putting her in with a couple of small treats or a kong with a little something in it, it will give her something to do for those first few minutes and may help her settle also.
It sounds like you are doing a great job with her, keep up the good work.