Thanks Tracey and Mary.
Well this morning she wanted to sit in the bathroom window again. One thing I'm noticing about her is her meow is much different now. I actually sat in the bathroom for a while to pet her when she'd let me. She lets me pet her but not like before. She used to rub her face all over mine. Hopefully she'll eventually get back to that.
But yes, she seems a little less upset about the whole situation. This morning she was sitting outside Jax's room and when I looked out at her she meowed at me. LOL I think this weekend we might try a brief introduction without a gate in the way. We will see!