Ahhhh I can understand, while you are definately not the worlds worst puppy trainer, your puppy is just confused by the amount of attention she's received.

Often times these pups come into our homes and we lavish attention on them while they are still very young, than we start to venture out and they get totally confused by it. Often times when I hear of this degree of separation issues at a young age I suggest crate training. This is getting them used to the crate, and you start out while you are in the room with her. And then you do things like have a shower while she's in the crate, pop out for 10 minutes etc.... just get her used to being in the crate and feeling safe. You can pop the crate where she sleeps at night & have her sleep in the crate. With our lab, this crate was in our bedroom for the first month she was in our house and then we gradually moved her out into the lounge room in the crate.... Then after the baby came she was used to sleeping in the lounge room rather than our room.

Also everytime you leave or come home pretend its not happening. Don't run and get so excited when you first come home, but ignore her for the first few minutes until her cortisol (stress) levels lower and then greet her. When you leave, don't make it a big deal, but pop a pigs ear with her and leave while she's entertained by it.

Training training training... this builds her confidence and she learns what is expected of her, so rather than trying to work it out she knows. There are some amazing courses out there, but trying to find one that is a delta society course.