Emphasis to focus on cultural alignment should come from top leadership which leads to creating and implementing a plan to drive the activities to understand and adhere to cultural differences between the two companies. Focus groups, interviews, observations are the methods that can be used to understand what is important for employees from acquired org. Team building exercises in informal settings help to achieve the goal too.
I also wonder if the creation of culture ambassadors is an option. I have worked in businesses with strong culture differences being observed between different countries. To improve communication and cooperation, we formed project task forces that made up of a diverse team and they would spend time on a specific project across various manufacturing sites. These teams not only provided some excellent technical solutions to improve efficiencies in the factories, but also shared a lot of great cultural insights. This ultimately, led to a much deeper appreciation and respect across the teams and knocked down virtual walls that were in place.
The organization culture can be defined through its code of conduct, this can be reflected thru leadership at all levels, sustain a culture where ethical conduct is recognized, valued, and exemplified by all the employees.