Daron, having met your dog I can say without any shadow of doubt she has fear and confidence issues. It's why she would stand back and bark/growl at visitors but refuse to come near -- with your description it seems like she has quite a case of it. I think I still have a book I can send you on helping her learn to trust; the one I was gifted with by another dog owner when my big guy was a pup. I have your address, so if you'd like I can drop it in the mail. When I first met her she reminded me a lot of him when he was young. FWIW, he's a good dog now. Still has his inborn personality to be more cautious, but has learned to greet people without being fearful most of the time. It can be done.
One thing on teaching commands is to make sure you're setting her up to comply. So, for instance, if you want her to learn to come, don't say "come" unless you can enforce it. So in this case you would want to practice on lead, so you say "Come" once, and then if she doesn't comply you help her do so by pulling her to you with the lead and then praise. If you want her to sit you teach her when she is right in front of you so you can help put her in position upon giving the command. Another good way to teach commands is to give them as the dog is naturally doing the thing you want. If you see she's about to sit down, as she does it say "Sit" and then "Good Girl!" make a big deal out of it whenever she does something well. Use treats liberally with her. Even fearful dogs can usually be motivated by food. When my big guy was young I kept hot dogs in the fridge, precut into small pieces in a ziploc. Those were his favorite treats so whenever someone would pull into the driveway I'd pull out the baggie of hot dogs and give them a fistful. He could have all he'd take from the visitors. In pretty short order he came to associate strangers with hotdogs.
On the going to the bathroom in one spot, she may be more successful if you make that spot smell different than the rest of the yard. It's hard for a dog to understand the difference between one area of grass vs another area. To them it all feels and smells the same. So maybe sprinkle some pine shavings in the spot you want her to go, and then keep them refreshed so it's clear to her that this spot is different. That or just let it go. With a sensitive/submissive dog sometimes choosing your battles is even more important than usual. As long as it's not in the house it may not be worth worrying about.
And on breeding, even if you're not worried about placing the puppies, etc. one thing is that she can pass her temperament along, but another entirely is finding a stud. Health problems -- especially hip problems -- are very common in GSDs and any breeder who allows you to use their stud on a mutt ***** probably isn't going to be hip certified.