I know ZERO about breeding/stud fees, etc. so keep that in mind when I say:
WTF?!?! Why is it so important to her that the pup is a female if she's just going to turn around and SELL it? I know females go for more, but not that much more

And how can she be so callous? I don't particularly think that letting the stud's owner pic the best puppy is very fair either, the female does 99.9% of the work and assumes 100% of the risk.
I'm SO glad that I don't have any interest in breeding, other than looking at everyone else's puppies and pregnant Mommies and ooohing and aaahing over them
I hope that you can come to an agreement with her. How is your girl, is she feeling okay?

I'm sorry that you lost some pups, that's so sad