I'm going to try very hard to be nice on this one, but it's a stretch for me. Ditto for me.
I have a rescued golden, one who was kept in a chain link kennel with a dog igloo in it. Not quite the same circumstances as your situation, since he rarely set foot on grass, but the storm phobia was astounding and still is. Go crawl into your dog igloo in a thunderstorm and listen to the magnification of the raindrops or hail, not to mention the thunder.
It won't be pleasant for you,and you have the ability to know what it is. So think how much more frightening it is for your new dog, who has luckily bonded with you but can't figure out why in the world he's left outside in a storm with all that terrible noise or at all. My two cents.
If he happily went in the crate in the garage, why not happily in the crate in the house?
That explained a lot...
My son was a severe asthmatic growing up, so our previous golden wasn't allowed upstairs on the bedroom level of the house, and my son had to wash his face and hands thoroughly after playing with the dog.
If this dog is as nice as you say, your wife will come around quickly. Get your daughter involved in the training, nothing is more precious than a child and a dog together, playing and training.
It has taken lots of desensitization, Rescue Remedy and more than a bucketload of love to make my dog "normal". I forgot to mention the extraordinary amount of money to repair his broken back, courtesy of his previous owners, but hitting him with a baseball bat or a pipe was just an extension of keeping him terrorized in a concrete kennel. I'm very proud of you for rescuing and paying for those and for giving all and loving those animals. Good for you!
I'd like to say that I don't mean to be harsh here, but I actually do. Well, congratulations are in order! You've succeeded in being harsh. But let's move ahead with what this forum is about, please.