Regarding the 7 mailboxes - have you looked at hidden recipients on the 5.5
You need to check if there might be some hidden mailboxes that you haven't
migrated. If you look at the 5.5 private information store you will also be
able to see which mailboxes are left (might be antivirus, backup and system
mailboxes which you don't need).
The replication which you should perform as one of the last steps is between
the SRS and the active directory. The SRS is the 5.5 emulation which runs on
the first exchange 2000 server you installed.
I went to remove our last 5.5 server exactly as per Q284148.
Attempted to use ADC Management Tool to do to perform the final
replication however discovered that the CA had been removed.
The last 5.5 server had already been decomissioned and no longer
exists so it won't allow me to create a new connection agreement with
it (States that the 'Exchange server specified on the connections page
So now this server is but a phantom haunting the System Manager... How
can I get rid of it??