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The issue with Exchange 5.5 on Active Directory domain controllers boils down to an LDAP (Lightweight Directory Access Protocol) port conflict. Exchange 5.5 servers, which host their own directory and directory service, listen on TCP port 389 for LDAP requests -- so do Active Directory domain controllers. Because TCP ports cannot be shared, you end up with a port conflict. The solution is to change the port used by Exchange prior to upgrading your PDC. To do this, see Microsoft Knowledge Base Article 321501, HOW TO: Change the LDAP Port for Exchange Server 5.5 in Exchange Server 5.5 .
At this point, you can do an in-place upgrade and move to Exchange 2000. But I would recommend installing a new member server with Windows 2000 Service Pack 4 and Exchange 2000 Service Pack 3 and then migrate by moving mailboxes. Running Exchange (especially Exchange 2000) on an Active Directory domain controller is not recommended, so if you can migrate to a new server, you'll be in great shape.
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