If you are getting the following error:
'The component "Microsoft Exchange Messaging and Collaboration Services"
cannot be assigned the action "Remove" because: - One or more users
currently use a mailbox store on this server.'
then the odds are good you have an item in AD that is still pointing to the old Exchange 2003 server. Here's how you get rid of it.
Just open up ADUC, do a find, create a custom query and paste in the command you see below:
Then select VIEW, then choose Columns.
From there you can add in the extra values needed to find out which account is still showing old Exchange 2003 data. Just add in both attributes with Exchange on them. Redo the Find Now and you'll be able to sort them by server name to find out the offending accounts.
During my last SBS 2003 to SBS 2011 migration it turned out to be the SBSAdmin account that I had created during the migration steps.
Once these accounts are removed or corrected you can continue your uninstall of Exchange 2003.