She's 9 weeks old. Yorkies should be with their mom until about 12 weeks. Your breeder shouldn't have let her go that early!
I think this is the major part of your problem is she's probably going through separation anxiety because she's so young.
I'm hoping others will have suggestions.
Mine would be to be with her as much as you can for the next two-three weeks and not worry about the potty training so much at first. If you need to contain her make sure there are pads everywhere, and if you can put her in a little kennel by your bed so she feels close to you that might help.
You will get through this but understand there's nothing wrong with her - she's just too young.