Another thing with crate training is don't take them out when they are crying or barking. Wait until they are quiet, otherwise they may associate "I bark and I get let out" and keep it up.
She will probably quiet down soon, but it can be nerve wracking 
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Exactly. This is a terrier puppy--she's going to push the envelope by nature of the group of dogs. The thing a new puppy owner absolutely cannot do is give into the dog when they are having a puppy temper tantrum or else they run the risk of going down a long painful road of the dog manipulating their every action while it runs wild causing intolerable havoc and destruction (ok, I'm exagerating, but you get it).
There was mention earlier of a HUGE crate---I actually think getting a smaller breed puppy a large crate like that can cause anxiety in some of the dogs. Dogs by nature are "ground dwellers" meaning that most of the canid species have puppies in relatively dark spaces underground. A large kennel without walls closeby can create a feeling of anxiety much like being in an open space. By initially using a smaller kennel with more solid walls (not wire, but a versa kennel type kennel) you mimick the burrow effect of the dogs nature. This is also similar to the nests that domestic dogs will make in boxes with towels/blankets etc. As the puppy ages, move to a larger kennel with open sides so the dog can see out and you can interact with the dog while its kenneled, just the same way a wild dog pup as it matures starts to venture out from the burrown. Second in a smaller breed puppies, giving them a huge space gives them a great place to shit and then back away from it. I think you can actually complicate house training/kennel breaking by having a kennel that is too large with some dogs.
Exercising the puppy before it goes to bed will work. Also taking half an hour or so for light exercise when you do the 3 AM poddy break (a must for housebreaking a puppy this young---they cannot hold it overnight, no matter how much you want them to, they have to have an opportunity to pee and maybe poop). Just be aware that the middle of the night session might get the dog more wound up and instigate an outburst. You can combat this by making that time a "strictly business" time where they go outside, they get their treat, and they come back in to bed, no ifs, no ands, no buts.
If the yapping continues, you can try distraction with something like a tincan filled with pennies or a boat horn (if you dont have any neighbors). the idea is to give a sharp distracting sound when the dog howls, followed with a firm NO. I'll be the first to say, this does not work with some puppies, so you have to use your judgement on using it.
