Manually Removing an Exchange 2007 Organization
As you are probably aware, Exchange 2007 can happily co-exist with Exchange 2000 and Exchange 2003, and you can take a fairly extended time to execute your migration.
However, you can't directly upgrade from Exchange 5.5 to Exchange 2007. You have to go through Exchange 2003 first.
There is a slight "Catch 22" issue...assuming you didn't read the installation documents. What if you went ahead and installed Exchange 2007?
Once you've done that, the Exchange 2007 setup doesn't see any of the Exchange 2000 and Exchange 2003 schema changes to Active Directory and assumes a "greenfields" installation. Therefore, it goes ahead and creates the schema the way it wants it, and doesn't create the items in Active Directory that are necessary for the Active Directory Connector to work to connect to Exchange 5.5.
Now, you can't install Exchange 2000 or Exchange 2003. Their setup sees that the schema has been extended to a version beyond their's, and the organization object is present, but the organization doesn't contain some of the child objects they require - so the setup aborts.
What do you do?
First of all, you smack yourself upside the head for not reading the installation prerequisites and documentation.
Secondly, you completely remove the Exchange 2007 server installation by following this Technet article.
Thirdly, you remove the Exchange 2007 organization by following this Technet article.
Now, you can install Exchange 2000 or Exchange 2003.
But please read the documentation first! 