You keep giving her attention when she cries (staying in room, soothing her by stroking her, returning to her etc.). This is teaching her that whining = you coming to her attention.
As rough as it is, she needs to learn that you're not always going to be there and her crying won't change anything. It'll be a tough few days/weeks when she goes through this process but she will learn.
Anytime she cries/whines, ignore her completely. If that means you have to put her in another room when you sleep, so be it. Definitely do NOT spend entire days with her by your side, even if she's crated. This will create huge anxiety and separation issues later in life. You need to build her up to accepting you won't always be around. While crated, gradually move her further away from you, extending the distance and duration each time. Put her 5 feet away for 5 minutes, then 10, then 15 etc. Then increase to 10 feet. Eventually you will reach a stage where putting her in another room altogether will work. Leave her alone in a separate room for up to an hour or more on her own, with toys etc. to chew.
Most importantly, praise her when she is quiet. Give her a treat if she stays quiet for 5 seconds, then 10 seconds, then 20 etc.
Eventually she will build up to staying quiet for extended periods, in other rooms etc.
As for sleeping, you have to stay strong. You cannot react to her whining, ever. If she needs the bathroom, allow her to go but then put her right back in the crate.