Sounds like she's always up to no good in the neighborhood! (sorry, dunno why I am referencing Fresh Prince theme song)
Have you had a chance to spend time with her after work for training sessions? Her jumping/pee/poop behaviour might stop if she's getting some training attention from you.
I can't imagine how furious I'd be if I came home and my little ones jumped the gate and peed in my bed! OMG!
At least she's sleeping well and not keeping you up through the night! Happy for you for that part.
I've heard that some Yorkies can jump and/or climb over gates. If she's bored and doing her wild-child act, being in a new place and all, I wouldn't be surprised that that's how the poop got over the gate and then she went back afterwards. Both of my Yorkies can jump! Actually before bringing Scottie home, my breeder told me he had jumped a gate already and told me to be careful. When Casie first joined us at 3.5 pounds, I witnessed her jumping up onto her 2' crate. She was so determined! I used large moving boxes and stacked them up. After some time, she stopped.
Since yours seems to like jumping too, I would try to Yorkie-proof it; they can be such sneaky little devils! Do you have some things like big boxes around the house you can stack up for a higher, solid wall? You might have to do something like that for a while to deter her from doing this. One, for the potty training period, and two you don't want her to hurt herself from all this mischievous jumping!
Do you leave them with toys inside the kitchen? Have you tried treat dispensing toys? Those are great to refocus their attention away from all the escaping. I used to leave Scottie with a treat dispensing toy each time I left, so he has always been excited while in a super calm manner when I left (he had to lie down in his crate and stay until I gave a command for him to get it once I was at the door). Maybe if you associate the kitchen with a treat dispensing toy, she'll like being in the kitchen more? If you wanna try that out, make sure you only give that to her in the kitchen while you're away and no other times.