Everyone here has given some great ideas, and I may repeat a few of them , sorry.
I agree with changing the feeding to twice a day, 1/2 in the morning and 1/2 in the evening. I feed dry food only, and one that is hard and good for their teeth, helps to cleen the teeth from the hardness and the shape of the food. Wet food will cling to their teeth and eventually cause problems.
I tried those little pills to keep mine from eating her poop or any other dog's poop we came across in the dog park,(many folks too lazy to clean up after their dogs). Didn't work. We just clean up afterword as fast as possible, so it is not around to tempt and stopped going to the dog park. I learned to teach her to "leave it" when I see her going for something she shouldn't when we go for walks.
I am up very early too, so morning walkies are out for us too. I do let her outside though and I tell her to go pee pee and poop. Then reward her when she does! Lots of praises, and a very special treat that you only give for that purpose!!!
When I get home, on goes her leash and out we go! Again, train her to do her thing, name it as she does it, so one day she will learn to do as you say. I have seen many a show dog being told to go potty outside the building when they are being exercised before going back in to the show ring. So it is possible to do!!!
My dog rarely eats during the day, she mostly eats when she sees me eat. She'll eat a bit at breakfast and the rest at supper.
I do give my dog those raw hide bones, when they get too messy looking or torn up too much, then I throw them out, same with any of her other chewy toys. She loves chewing on them and I give her ones big enough for her to carry , but not small enough to tear up too quickly or swallow easily.
You could just give her one or two toys at a time to chew on during the day. change them out once or twice a week. I wash the squeeky toys on gentle cycle and "hang them out" to dry. I am not sure they make the Automated Kong tossers small enough for a Yorky.
Yes, that schedual will help as well, I have several books that list them, I haven't used the ones in the book,s but don't give up on the train the dog in 7 days, it has several good scheduals and suggestions on how to train your dog, you just have to pick the one that suits you.
There is no magic way,you just have to pick a way that is good for you and keep at it until the dog "gets it" The clicker website has several good ideas too on house training.
I think crate training helps to keep the pee and poop confined away from the rest of the house,but a full bladder and colon, can't be stopped. Regulate what and how much goes in and it will help a lot with how much and when it comes out
If you ever get a pen, get one tall enough to keep your pup from jumping out and I put a large rubber mat,(a long car mat like you'd put in a van) under ours and it confines the mess and makes it easier to clean up. You can always take it outside to hose it down too! You could also use an old vinyl table cloth or shower curtain!
Good luck and keep trying, she 'll learn eventually