Regardless of your design, you are correct that Active Directory Connector (ADC) will be a key piece of the design....
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It is likely that you will need 40 different Connection Agreements (CAs), one for each Exchange 5.5 site. If you have the network connectivity, it would be easier to manage if you had one or more servers dedicated to this task at headquarters. Active Directory Migration Tool (ADMT) could do the job, but there are some great tools available to help restructure things once you have a strategy. I happen to like Aelita's solutions.
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