I think that Ginger899 came up with the answer to your problem. When I got my Yorkie she was 6 weeks old and whined all of the time. I picked her up and held he and when I went to I would put her on the bed in my arms and she would quiet down and sleep the whole night. I figured that she missed her mother considering she didn't start crying until after I bought her and she was separated from her mother and siblings. I would place her close to me and she stopped her crying. That was 10 years ago and she still sleeps with me and is usually on my lap or within a few feet of where I'm at. My point is if she has some type of physical contact or maybe even something that her mother or you have touched she may quit crying. I find Princess laying on top of my clothes or on the bed close to my scent when she does leave my presence. I hope this helps to solve your puppy crying problem.
It sounds like you are doing your very best for this little pup, and have already sought a vet's advice.
I can understand what you feel about taking her back to the vet, to receive the same answer and have to pay a big bill!
I'm sorry that I don't have personal experience with very young puppies, and so can't be as helpful as you need someone to be.
You said the "mother CAN feed them"? I guess you meant to type "can't"?
You say she stips crying when the mother cleans her or when she gets tummy rubs from you. It may be that she craves physical contact of some kind, and misses the feeding contact with her mother's body.
If she were crying from pain, she would probably continue to do it even when you gave her tummy rubs or when her mother cleaned her.
But I am guessing here really.
I hope someone with more experience will contribute here and help you