Your puppy seems to be causing you some worries and stress. I'm sorry he arrived to you sick. I think you said you got him from a pet store? If you think about what he came from and really try to look at what his first few months were like you might be able to understand more about him being a bit more difficult and may have more health issues. I'm sure it was hard for you to learn about where these pups come from and I'm sure you paid a lot of money for him.
I have never had mine wake me up barking in the middle of the night for no reason. Baby pups don't tend to bark that much. At least mine didn't until they were about 6 mo or so. It sounds like he ( WHAT IS HIS NAME?)
just wants to play. Or wants to sleep with your mom? Trying more exercise before bed time might help.