Hey there! Nice to hear that you are enjoying the game! =)
As for you questions:
1. I try to keep girls' event cognizant of the main plot if not directly tied to it. In your example, Gwen will not come to support you before the second Trial if she is currently mad at you (at least she shouldn't. That's be a bug). And in some rare cases there will be different variant of events depending on your relationship status with a girl.
2. At the current moment, you only get one chance to invite a girl on a date and the storyline is blocked forever. Same happens if you skip the date. In the future I am planning to add a couple of "second chance" events which would allow you to revive a ruined storyline with one of the girls.
3. There are no house exclusive girls, but for each house one girl in unavailable. For Ruachan, it is Violet as you have already noticed.