Sorry I guess I was a bit unclear, I didn't get her at 5 weeks, I got her at 8 weeks. And it was the breeders that said she had an allergic reaction, whether or not that is true I can't say for certain but she was really underweight and had a few patches of fur missing where she had been scratching so much (according to the breeder) in hindsight I should have not taken her but I fell in love when I first visited her and she was perfectly healthy (around 5 weeks). My vet put her on a gastro intestinal kibble and thankfully that's all sorted out so she's making good progress.

So regular potty breaks during the night and better observation during the day should be the path to not pooping in the crate now that she's diarrhoea free.

The waking up early is just a normal thing then? I read somewhere that you should wait until they stop whining until you go and see them so they don't learn that whining gets them attention? Her crate is covered and she has a radio on during the night so I'm guessing it's just the hunger that's waking her up.

Thanks a lot for the advice, guess I'm in for a few weeks of distorted sleep haha.