I think you are wise to investigate when your child has a problem in school. I think you might have made an error, however, in telling the teacher outright that your son thinks she is a mean teacher! That's just going to put the teacher on the defensive! It might be more effective to say that your son seems to be having difficulty adjusting and that he can't articulate his problems too well but that you think he may be reacting to discipline or taking things to heart. That's at least a basis for conversation. Then you find out, in the conference, where she sees him shutting down or retreating or not being an active participant, where he seems frustrated or angry, and so on.
I agree with those who have said that school has only been in session for a month. It always takes kids and teachers a while to get settled in and used to each other. That she is a first-year teacher is reason enough to give her some time. It's also very typical of teachers to establish disciplinary techniques and standards from the beginning of the year - if the kids get out of hand early on, it's much, much harder to rein them in after bad habits have developed. Kids can earn privileges by engaging in cooperative behaviors - a good life lesson.
I have no idea why you felt it important to list his reading scores and all his intellectual achievements. This has nothing to do with the issue, does it? There's a huge difference between a child's intellectual skills and his social skills, adaptation abilities, and articulation. You've said that, despite his book smarts and test smarts, he cannot explain himself! So that's where you need to dig more - his communication abilities. You just don't have enough information to know where the problem is. I'm also confused about why you are going down the "no labels" road here - has anyone suggested that? Has the teacher or the principal upset you with anything in this area? You state that you are "fearful" about long term effects - is there a reason why you are particularly fearful of labels?
In 3rd grade, teachers DO ramp up the expectations a bit, and kids have to grow up a little more. That will happen again every year and it's time for your son to learn that he is growing up, has more responsibilities, and more work to do. Does he have an unrealistic expectation that school is play time? Is there a group of kids in the class who are having trouble with this, and your son is reacting?
I think some of his comments merit investigation. He calls her "evil"?? Astounding concept for a 3rd grader. He's saying when SHE is having a good day and when she isn't? And that she got a phone call that upset her? I'd investigate those assumptions a lot more thoroughly.
Overall, I think you have to approach the teacher, principal and parent as a TEAM who are all working for the same thing, rather than starting out with an adversarial relationship. You said you thanked the teacher for changing something and making things better - but maybe SHE is consistent, and your son is the one having different reactions. Just because he had a good day doesn't mean she changed her style - it means he's in 3rd grade and he has different moods, and it also may mean that the other kids are behaving better so the whole class has a better day.
I think your son needs to spend less time on whether the teacher is having a good day and is being upset by phone calls, and less time worrying about the other kids getting corrected and redirected by her, and he needs to understand the difference between a teacher raising her voice to be heard above the din and actually yelling AT kids. When he can manage these distinctions, and can focus on his own behavior as well as being able to articulate things more, I imagine a lot will improve. It's important that HE not label the teacher (evil, having a bad day, etc.) and just explain the FACTS of what happened. That's where you're not getting enough information yet to make a decision. So I think it's way too soon to even title your post "when to change a teacher" - you will be much better served by getting your son to explain what happened, who said what, who did what, etc. rather than labeling and categorizing adult rationale when he's just not old enough or mature enough to do that.