So if you misunderstand the setup instructions and don't run setup /pl BEFORE you run setup /prepareschema and setup /prepare domain, is there any way to rectify the permissions manually? If not, what is the best procedure for restarting the exchange 2007 install with an existing exchange 2003 infrastructure?

Hi, Don't worry: setup /PrepareAD will automatically perform the PrepareLegacyExchangePermissions step in the domain where the /preparead (root domain)if not run before. If you have child domains in the forest you must still run this /pl command in each domain. Leif

OK, so I am installing Exchange 2k7 into a child domain and not into the root domain. Do i need to run this command again on the root? We have one exchange 2003 server in the root, and one in the child. The server in the child domain is the one that is being replaced by exchange 2007. The 2k3 server in the root will be remaining a 2k3 server for the foreseeable future.