Need help with 2 things (peeing and sleeping)

Hi y'all,

I have a 13 week puppy that we've had since 5 weeks (long story. She's a rescue. We also don't know what breed but she's a smol girl)

She's had two UTIs, which I don't think has helped the potty training development, but they've been treated.

1. She really is just not getting the not peeing in the crate. She can pee outside and she gets a treat and praise and then I bring her in and she pees in the crate right away.

2. I'm not sure if she's old enough to be sleeping through the night but she wakes up every 2 hours in the crate whining. I take her out and she pees. She comes back and takes half an hour crying in the crate before she falls asleep. I am run ragged. I have taken her to the vet to get checked out in case she has a kidney problem or something. They did a bunch of tests and imaging and say she's fine.

Pleeeaaaase can I have some advice? I'm going crazy here. I just want to be able to have her around the house or sitting next to me without having to worry if she's going to pee or poop on something.