You seem like your on the right track. I would caution that you don't need to know everything about every aspect of the organization to accomplish the goals of the project. It sounds like you primarily will need to focus on data and reports. Of course, if the organization is small having some knowledge of the organizations goals and purpose and an understanding of the roles of each department won't hurt.
But to come back to your main focus, consolidating multiple databaes, here are a few pointers:
Hopefully, this will help get you started. I tried to keep it high level here. I'm sure you will have other questions as you dig in.
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