How to help a whiner/timid puppy.. gain confidence?

I just purchased a 9 wk purebred border collie puppy. I want to use her for agility and freestyle events.. however she is very timid and whines alot. There is no way I can socialize her with how timid she is currently. She whines when she is nervious/scared or if she can't see me. Even after 2 days she would rather be in her crate then with me as she uses it as a security blanket. When it comes to the whining I ignore it and her inless it becomes excessive or howling, then i clap and that seems to catch her attention and she calms down. She is VERY smart and a good puppy, I just need help knowing what to do to stop the whining and get her more confident. What I have done with confidence is just alot of calm petting and playing and spending time on 'her level' as she hides when I walk around to much. I give her alot of calm praise and treat her for going potty and coming when called. I just have tried to keep the household calm for now!