Hi - no real advice for you, I'm afraid, but just wanted to chime in to say that I think this is something that a lot of historians deal with in one way or another. In fact, last chapter I got told off for going too far the other way and it being too much of a straight historical narrative. At the moment I am turning it into an article and structuring it so it works both thematically and chronologically is a complete nightmare that is making me lose sleep! I think it is something that only comes with practice and something even my supervisor has confided that he has real trouble with - and he's a professor!
So, I know the feeling. And probably so does every historian out there! I know that doesn't make it any easier, but...