It seems to me that this dog was raised as a pup being allowed to go potty where she slept. Now that she has done that she finds comfort in it. I would do just like you've been instructed here to the letter.
If in fact you are doing all these things like controlling the amount, and time she gets fed, and the scheduled potty breaks from the crate then I would try it the exact opposite way around.
The dog is having a movement inside the crate because it is getting kind of freaked out in the crate and causing it to go to the bathroom (like an upset stomach from being nervous). I would keep the dog outside and bring it in only while I can watch it. This way you can correct it for going in the crate. If you can't watch the dog while she's in the crate then don't put her in there. If she is getting an upset stomach from being in the crate, try leaving the door open and put her food and water in there so she can begin getting used to the idea that the crate is o.k.
The success of this depends on if you can be diligent enough to keep your eye on the dog so you won't allow anything but success. Always if possible set your dog up to win.

 Quote: connie sutherland

Just read the o.p. again.

Not clear what this mean: "it seems she wants to be outside."

Also, I had missed the ear infection part. How is the ear infection now? I'm asking for obvious reasons, but also because I adopted a dog years ago who had indeed become deaf due to ear infections (secondary to allergies, after many years on crap-in-a-bag grain-based foods).

, can you estimate the amount of structured exercise she gets daily? I mean walks, play with a human, even short motivational upbeat obedience training sessions.

All these things have direct bearing on the challenges you mention. Also