Wow, I am sorry to read this, it sounds like hard work.
How much exercise does she get?
Can she start any puppy training classes? This may not help with the whining, sleepless nights etc but it may help with regards to her listening to you more.
I would try crate training her again throughout the night, can you move her cage away from the neighbours side of the house? I would let her whine (not if it effects the neighbours, of course)
As for toileting I would go back to basics, outside every morning, after every meal, if you can see any tell tale signs. I would say "clean girl" as she goes and maybe reward with a treat every time she toilets outside. If she wees inside I would just put her straight outside the second you see her going.
I would walk her often, short walks while she is still young, and train her basic commands in between to keep her stimulated. I would get her a lot of the toys she likes to chew on.
Can she go to day care one day a week to burn some energy, get some socialisation?
Hope this helps a little bit, my puppy is almost 7 months old now but we are incredibly lucky with him.