I don't use AA. However, I do believe that most of us do have underlying issues that don't just fade away with ..."dry sobriety"; if anything, they seem to be intensified by it.
I'm by no means an expert on the lingering biochemical effects of substance/alcohol abuse, but it's my understanding that such effects, like you mentioned, are mostly cognitive. The emotional part... I guess it can be worked on?
Have you voiced your concerns to your father? Maybe it's something you could talk about with him, if the two of you are willing to.