Seem to have come to a happy medium. Gracie stays in the basement (finished and furnished) while I am at work and overnight. She is perfectly happy down there and happily goes down each night with just a point of my finger. My husband stays down there so there's company even though she isn't too fond of him.
Boone is indecisive as to whether or not he accepts his sister again. Most of the time, he will ignore her or lick her head in acceptance but occasionally, he will hiss at her. The weird thing is, he will hiss without showing any sign of being scared. Yesterday, he was literally half asleep on my pillow when Gracie walked into my room. Boone opened one eye, hissed, and then went right back to sleep. Guess he just wanted to let her know that he hasn't forgotten his whopping by her.
I also upped the Feliway diffusers in the house. Went from one on each floor to three on each floor. I also had no idea that those needed to be entirely changed out every 6 months so I'm sure ours weren't working as well anymore. That also seemed to help calm things down.