There needs to be a transition project headed up by influential leaders, and they need to set out the synergy goals - things like what important services or features are key, which side will lead important aspects in the future etc…

Without a clear plan and good communications down to the lowest levels from above there are a number of ways chaos can ensue… not just technical differences but as you say org and people issues mainly.

Once the commercials are agreed someone needs to take the reigns on the transition aspects ASAP.