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This is a complex environment and an opportunity for simplification. Though there may have been reasons for the many sites and domains in your environment, you should confer with someone knowledgeable in Active Directory (AD) and Exchange design to see if it can be made less complex. An assessment would look at the organization, network, loads and user requirements. You might find that regional or centralized servers could significantly lower the costs of upgrading all that hardware (assuming that the current servers may not be powerful enough for Exchange 2003). Research and a formal project plan will pay off here.
Regardless of your design, you are correct that Active Directory Connector (ADC) will be a key piece of the design. 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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