I'm going through something similar now, except it's only been two weeks for us. We adopted a little kitten and our two older cats are in various stages of dealing with it. Our younger cat has accepted the kitten, but gets into dominance play with him that gets very rough at times - he'll hold him down and bite at him until the kitten cries out. But he'll share food with him, play with him, lie down with him, etc. so I'm not sure how much of that is really aggression.
Our older cat just doesn't want to deal with him. He's not being aggressive at all, but he growls and hisses when he sees the kitten. And yet, they will sleep in the same room, and he will eat in the same room with him - but if the kitten gets close, out come the hisses again.
My husband really wants to encourage them to be closer and to get over it, but I keep telling him there's really nothing that we can do to urge things along, and that urging things along might backfire on us. Is there anything we can do, or should we just leave them to it, even if it takes a long time?