Answer

Let me start by saying that I think a good connection is very important. As for the religious matters you mentioned, it is definitely worthwhile to clarify them thoroughly between yourselves. If she is also prepared to violate Jewish law, that is problematic. But if she does not intend to violate Jewish law and only wants to conduct herself in a way that doesn’t appeal to you, then I think there is room for the two of you to reach a compromise.
What you call a Torah home may not be something she agrees with. That is worth clarifying. If there is no agreement on that, then it is not a side issue as you described.
The discussion of these matters should take place on two levels: 1. Consideration for you. 2. The direction and character of the home. (Pants, for example, are not a problem at all in my view. But it is worth checking whether this is only a fashion choice or whether it expresses a different religious approach that will also show itself in more substantive issues.) Both of these levels are important not only in themselves but also as an indication of the relationship between you. If these issues will bother you and she does them anyway, then the connection between you is not as complete as you describe. I understand if she says she will not accept dictates because she wants to decide how to dress, but she still should take your feelings and wishes into account and consider them. And needless to say, you should do the same for her, of course. You should give in on matters that are not essential, even if they bother you.