As a retired behaviorist/trainer and German Shorthaired Pointer Rescue chair for TN/AL/KY, I'd like to add a few things I learned along the way.
1. Never, ever, under any circumstances use the phrase "Bad Dog!" That implies the dog understands what "bad" means. They don't; they might look guilty but it's because they read your body language and vocal tones. Plus, it's negative.
2. Breast cancer chances increase with each season. Prostate cancer chances increase when males are left intact. So I recommended clients spay bitches at one year or after first heat; whichever came first. Neuter males at one-to-two years unless marking, aggression or unwanted sexual behavior occurred. If she were mine, I'd have her spayed and tell anyone who might want her there's no cost but you do need to be reimbursed for the spaying. Never trust anyone to honor a contract. Not everyone is as diligent as you are. And not everyone even recognizes when a bitch is in season. *This was written before 15 but appeared after. Maybe the shelter would give you a paper like they do people who adopt from them (at least in TN they do). *
3. Rescue dogs don't know their names. So I used cheese or hot dog pieces. I'd make a quiet noise and when they looked I'd say their new name simultaneously with giving them the the cheese or hot dog. Biscuits are for treats for doing nothing and for sit, down, etc. But hot dogs and cheese are for name recognition and coming when called. Only say their name once or you'll have a dog like my late girl who thought her name was "Hannah Hannah."
My dogs don't know the word "come." They come on their names. "Come" is just one more command we teach them to disobey. Associating their name with special treats makes them much more reliable. Oh, you can use a squeaky to get their attention and then say their name. This gives you two ways to call them/get their attention. You *must* make learning their name a lesson.
After they turn on their name, walk a few steps, say name and reward. Do this for three days and then randomly replace food with "good dog." But always have the food in your hand. This is where most people train their dogs to only do actions for treats: They suddenly stop the treats; they must be gradually weaned off them. According to most studies, it takes approximately three weeks for a dog to have a behavior permanently embedded.
4. If they don't listen, never raise your voice. Either go to them or tap them on the shoulder to get their attention. This works with name recognition, too.
5. If they're afraid of something (like the grate), stand still and let them flop around like a fish until they tire. Hold your arm still; let them, not your arm, flop. Don't say anything. Just stand there. When they stop flopping, move a foot. Stop. Still not saying anything. If they run past you to get away from the "monster in their mind," stand there. When they stop, move forward. The key is silence when a dog is afraid. If you don't acknowledge the "monster," eventually they won't, either.
Dogs only learn what we teach them; good or bad. You are so smart to not yell. All that does is teach them you don't mean something until you yell. My belief is dogs do what you expect them to do. If you expect them to lack respect for you and what's yours, they will. Obviously you're not letting that happen. She will wind up a great dog and she's lucky to have you guiding her.