C..
I would say pick the one thing that "bothers" you the most. "we say please and thank you" (or whatever) and work on that for a couple weeks. Then move on to something else.
"tone" is hard for a three year old to understand (you can tackle that when she's a teenager - because she will replicate her same behavioral issues she is now... she'll just be bigger!!!!!). So, I would work on things that are concrete "we use nice words or we say nothing" rather than "don't be a smart-mouth" or "be polite"
For the glares, this might be something I might acknowlege "I see from the way you are looking at me you are upset." but, personally, I probably would let it go. I think if you are working on the other stuff, the glares will work themselves out.
Not sure if you have transitioned from toddler-mentality to pre-school-mentality. She may be wanting to make more choices and have more independence. That may be where some of this attitude is coming from. So try ramping up what you allow her to do and see if her newfound independence helps.
BTW.... I was serious when I said she will turn into this same person as a teenager. They've actually done studies that the same issues you have with toddlers/pre-schoolers are just versions of the same ones you will have as a teenager. It has to do with how the brain develops. So, take note of what works with her. You will need those same tools to parent her in 10 years.