In my experience, the hiding period was very short. My current cat hid for about few hours before loosening up and demanding to be put in my bed (he was around three months old too, but we got him from a breeder so he was already adjusted to people). All in all, the cat should loosen up quickly, but be patient with her. Be good to her and take small steps, especially if she's overly frightened.
Scratching the collar is normal; my cat still hates collars, after almost 9 nine years. If we put it on him, he refuses to move and then proceeds to scratch it and attempts to remove it from his neck (with various degrees of success). Sometimes he just accepts his fate, though.
About leaving her; well, yes, I'd say it's okay. Cats are solitary creatures and sleep most time of the day. While you're out, maybe she gets the courage to get out of hiding and explore her surroundings. We always left my previous and my current cat alone for at least 8 hours every day (school/work) and they were fine. We even leave my current cat alone for two days; we fill his bowls with enough food and water, clean and fill his litter and he's fine. Cats are perfectly fine with being alone; I'd say they may actually prefer it most of the time (of course, kittens always demand more attention for playing, but they too need a few hours a day of rest without us, puny humans, wondering around and making noise).
EDIT:
AndyFromMonday said:
Is there any way to get her to stop climbing on beds and such or is this just another little quirk I'll have to live with?
In my experience, no, but I know that some people manage to "train" their cats successfully. My cat is very stubborn and slightly naughty so he does it on purpose especially when we forbid it (and he knows what is forbidden for him to do, he just does it because he's a cat and thinks he can get away with it). However, it is possible to teach the cat that she can't do that. Of course, it'll take shitloads of your time and nerves.