Hi there,
I was wondering, is it normal for her to have just these 2 commands that she can do (not perfectly) ? Is there a sort of guideline for what she should have be learning at this age and the months to come?
I think they all learn differently, our 1st learned most of his tricks pretty quickly, our 2nd one not so much, he just doesn't seem to understand and I think has ADD 
But my question is, is this a bad place to keep her? Germs etc aren't the issue, I clean that place every day, the light thing worries me. I'm thinking of getting a mesh/fence type divider for the door, so the door could be kept open but she wouldn't get out. Does that sound like a good idea?
I wonder if you used a night light? we bought a gate but the youngest one knows how to scale all the gates and even his xpen when he wants. we bought the mesh but he tore that up.
Last week we went to the vet to get her shot, and she said that I could start giving her wet food,
I know ever vet is different, ours told us not to feed wet food daily, she said that hard food is better for them and it breaks up tarter build up on their teeth, I do feed some wet mixed with dry but not daily.
And also, I guess that she'll need more food then, so instead of a spoon per feeding, I'll have to give her 1 1/2?
we went from free feeding to 2 meals a day and it was just a transition, I assume you'll have to do the same thing. the food bag will tell you how much and divide that by 2.
Another issue we have is breath stink.. I know that you should give dogs the bone things for them, but is it too early for a 3 1/2 month dog? And what are the alternatives for fixing the bad breath issue?
I think their breath starts to smell really bad when they are teething, my first one went through that. we got bones, CET chew sticks (love these), bully sticks and my friends vet told her about petkin liquid oral care and I LOVE it, it has solved the problem and I swear by it.
Will she get it sooner or later that she must go to the bathroom to pee, or is there some extra training involved? She gets rewarded for peeing/pooping in the right place, and gets scolded for doing it in the wrong place.
it takes time, my first one was so easy but our 2nd one just doesn't seem to understand. I have read that you are not even suppose to say anything if you catch them peeing where they aren't suppose to, just pick them up and take them to the correct spot. Yorkies love any interaction and they really don't understand the difference when we acknowledge them, good or bad.
Jeeeez, I didn't realize I wrote so much
I hope someone will have the time to read and respond, it would be really helpful