Try to relax about the temp variations. Once you get it filled up with stabilizer stuff, it will settle down and be fine. Mine varied about 2-3° either way from 50°, and it was not a problem. The only problem is when the temp gets really warm, warm enough she wakes up. I don't think that would happen until it got to 60° or higher. A few degrees is not serious. If the cooler is in the interior of your house, you may have a bit more significant variation when you turn on your house furnace. If that happens just turn it a couple degrees lower. Please don't worry....you will be fine.
I did not use substrate, only newspaper, in the box. By the time she goes into the box, she will have had nothing to eat for at least 2 weeks, so isn't likely to poop in the box.
Personally, unless the top of the box is tight against a glass shelf, I would not cut it shorter. If it's against a shelf, maybe you could just remove the shelf. That's what I did.
Thanks, helpful info, as are the pics. I think I'm making progress, temps were a little more stable overnight. I think part of the problem is the hibernation box is on the large side (13x11) which means that's a good portion of the overall fridge space that just air space (prob 50%) which of course in turn causes temp fluctuations. My thought with making the box less tall, for instance 12" to 9", is that lets me add another full row of water bottles for mass. Right now the fridge looks packed but it's really probably just 50% because of the large box in there. I could find a smaller box, or also just keep working with this one, taking 3" off is pretty easy. Maybe I'll do both, IDK.
So just FYI as it is with the current box, I have about 4" of substrate in there (is that about right? That would cover her with about 1") which leaves about 8" of height over that, so that might be a benefit to reduce that to 5" and add another row of water bottles.
Also, I'll ad some water bottles today of different sizes to better fit in the nooks and crannies to reduce the voids.
Thanks for the info, and for reading (I like to give the logic behind what I'm thinking).