At first, their relationship could be strained. Logan may be scared by the news, and Rory might feel let down by his initial reaction. But as time goes on, they realize they love each other and want to make it work. They start going to prenatal classes together, and through this shared experience, they rekindle their love and build a stronger bond for the future.
Yes, there could be. Maybe some of Harry's friends from his original story like Hermione or Ron could be involved. They might be initially confused or even a bit against Harry's new relationship with Logan. Or there could be other mutants from Logan's world who interact with them and add more drama to the story.