The only way I could calm Blackjack at first was by putting him next to my bed and putting my hand on the top of the crate and have my fingers through the bars, that way he knew i was always there. I only needed to do this for a couple of nights then I slowly moved him across the room. I didn't continue crating him for more than a couple of weeks though, only untill he was 100% house trained. But thats personal choice, I wouldn't have it any other way, we sleep on my kingsize bed now, he manages to take up 80% of it though, god knows how lol. No one method works 100% for everybody, every dog and every guardian is different, see what works for you both and go with it, sometimes it takes a little trial and error. Have you tried putting something that smells of you in the crate with her? that may calm her, also a hot water bottle can simulate a sleeping buddy, just make sure the water isnt too hot, you dont want your pup to get burnt if she accidently pops it.
As long as you know that the dogs are 100% fine together that sounds like a viable option for when you go back to school, make sure though because with noone to intervene your dog may get pissed at the pup. And obvs, shelter and water always available. I imagine she would much prefer the run of the garden to being stuck her crate for so long, we ended up leaving Blackjack loose in the house after we'd had him about 2 months, he managed to break his first crate after he had escaped from it twice, he then escaped from his 2nd crate 5 times and we just gave up, he wasn't doing any damage to the house and he was just going to hurt himself on one of his escape attempts eventually.
*Blackjack was around 7 months old when we had him, and "apparently" crate trained but "un-toilet trainable", but i'm guessing he wasn't used to a crate seen as the issues that we had, so we basically started from scratch with the crate as you are, ironically toilet training him was ridiculously easy so i'm pretty sure his ex-owners were just lazy.
Good luck, and enjoy all the love and affection
p/s sorry if i came across as harsh in my first response i had just woken up and i was grumpy lol