Poor little girl! Sounds like she's having a hard time of it.
Believe it or not, I think your other dog is going to be instrumental in helping your new girl adjust. Dogs, whether socialized or not, seem to learn a lot from each other. We adopted a girl that had spent the first year of her life in a barn with no attention except getting fed and it took our other dogs a couple of months to teach her to play.
I would take the reintroduction of your other dog as slowly as you have time for. If you can get a collar for him that doesn't make noise, that might help if the jingling collar seems to put her off. Having them meet in a neutral area first might help. But I'd start that as soon as possible since you don't have a lot of time before the new semester starts. If you can set up a safe place for your new dog that the first dog can't get into, that would be great--when your girl needs a break, she'll have somewhere to go. Even if it means being behind a gate or in a kennel, she'll at least see the other dog and become familiar with him.
It isn't too unusual for a dog out of its element to not want to pee and poop. In our experience, for instance, English setter pups won't pee and poop out of the yard till about age 1. So she might not "go" while on a walk for quite a while. However, walks will stimulate the bowel, so after you get home, do a little training or just wander around the yard for a while and see if anything comes of it.
Keep up the confidence boosting exercises. And some joint training with your boy might help, too--as long as neither of them is food aggressive, running them through their paces together with frequent treats can be a great bonding experience for them.
Have you thought about where she'll be when you're gone during the day? Will she have the run of the house, or run of a safe room, or be crated...
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