Have you considered pee pads? I was adamant that my dog wouldn't use pee pads in my home, but now that I have him, it is really unrealistic to have him wait and hold it for so long. I mean, I go to the bathroom several times a day and will wake up at night too, so why would I not allow my pup to go too? I work from 8 to 5 and have a 40 min commute. That means I'm gone roughly from 7 to 6 everyday. It really is just too long between potty breaks.
I set up one potty area just for him inside our home. Just one. I show him where it is, tell him what I expect with the potty command he knows, and hope he follows through.
We're currently in the process or re-training since we just moved. New house, new setup. I can't expect him to get it right without some help. I don't crate either, but I do limit his space. Right now, he gets the master bath with piddle pads, bed, water, and toys. Once he gets use to that, and consistently goes on his piddle pad, I will allow him the bedroom as well. Once he shows me that he will always go to the piddle pad in the bathroom, I'll give him more space. We'll keep going until he earns free roam of the house. I've also used baby gates and exercise pens when we lived in an apartment to section off areas of the aprtment until we were able to trust him and slowly give him more access to our home.
When I'm home, he asks to go out. So really, the piddle pads are just for when I'm not there to give him a potty break. Otherwise, he's really good about letting me or any person at home know he needs to go out.
Also, I think you guys are actively ignoring her "I wanna potty" signal. Bringing her back to bed is not what she needed. She needed to go out. If you don't want to get up in the middle of the night, the last go out to potty walk needs to be right before bed.