I'm sorry you are going through this right now. I know how emotional this subject is. About a year ago, my FI and I moved in together. We had major issues with our cats getting along and it went on for months. We reached our bowling point and we took our frustrations out on each other. We were fighting all the time over about it.
From personal experience I can tell you that it will get better. I think you both just need to give it extra time and patience. Cats aren't good with change and it will take them a considerable amount of time to adjust. Hang in there, a year from now, the two of you will be laughing about it all.