In my consulting practice, I believe that one of the most significant ingredients that will ensure a successful partnership or merger is culture. Culture of course covers a number of behaviors within a nonprofit including the styles of the respective boards and senior managers. And managing, in today's environment (yes, I know, it's always about "today's" environment) is particularly challenging, as you well know.
I found an insightful article about culture and its impact on the success of an organization in the latest Conference Board Review that may be worth a look-see. Please be patient though: the story uses Lehman Brothers as the overt subject but believe me, the real subject is as the article's name suggests, Culture Crash.
And, should you not really want to know more about Lehman Brothers, allow me to share a part of the article's wrap-up that I think helps give the whole article meaning.
..a culture that is too strong can also end up too rigid and can shut out diversity, especially diversity of perspective. It can cause people not to trust others who may be unlike them or who haven't shared their experiences--confusing the unfamiliar with incorrect. A strong culture attracts people, both clients and employees (and board members and possible alliances). It also repels them, and the more passionate and proud you are of the culture, the more likely in the end you are to blind yourself to other potentially valuable points of view.