I think you have some good suggestions here. Dawn has some wonderful insight and that's very much how I did it with my son.
You need to prioritize which behaviors/habits are the key ones to change first. I'm not sure if your thought about taking away toys is because she doesn't clean up, or because she doesn't behave in other areas. I think you should sort them and toss what's broken, give away what's unused or outgrown, and store the rest. I used storage bins on a rack (you can sometimes find this at resale shops) and put photos on the side so my son could tell what went where. When he was really bad at taking care of things, I put them ALL in the attic. I don't think taking "half" the toys away solves much. I left my son his comfort items, his books, and arts & crafts supplies, but ALL the toys went into the attic.
I would leave her with comfort items - don't pack up her favorite stuffed animal or blankie, and I would consider leaving her the binky for now, while you work on behavior. It sounds like her attitude and disrespect is the worst - so make that your priority. For the time being, it doesn't matter if she sits in her room with a binky, does it? That's a separate issue.
If you sense that she is ready to potty train, do it - but be sure that she is ready. You cannot force that issue. Many kids are ready at 3.5 years, but some just aren't. It may not be stubbornness, it may be developmental. If, however, she IS trained and just won't go before you leave the house, then that is behavioral.
Definitely set up a bedtime routine and tell her what it is. Make sure you and Daddy are absolutely on the same page. Don't sit there until she falls asleep. Absolutely no dessert without supper no matter what, regardless of her behavior the rest of the day. Just don't have any desserts in the house for a while.
It sounds like the key behaviors should be listening, doing as told (you and teachers), eating her dinner with decent manners, going to bed, and cleaning up. I'd keep it to those - that's plenty. She needs to be able to succeed and not be overwhelmed with too many "new rules". That's why I'd leave potty training and the binky out of it for now.
You need to do what you can handle with extreme consistency. You cannot do anything halfway or she will learn that tantrums win out over Mom & Dad's resolve.