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Utilize the Exchange Deployment Tools for the entire migration process to streamline the deployment and reduce risk.
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Migrate using the Move Mailbox process whenever possible, and resort to the ExMerge process only if migrating between Exchange organizations.
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Install the Active Directory Connector on the first Exchange Server in the Site.
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Switch the AD domain to Native Mode in advance of the ADC setup and Exchange migration, to ensure proper replication of security groups.
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Use the site and server consolidation strategies in Exchange Server 2003 to significantly reduce the number of servers that will need to be supported.
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Rely on the ADC Tools to configure the connection agreements, and modify them only if there is a specific reason to do so.
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Leave an Exchange 5.5 Server in place only if it is needed to support connectors that are unsupported in Exchange Server 2003.