Renaming the domain is not a trivial matter. This can have impact on user all of the areas you described, plus also with the Outlook client authentication.
One way to do it and ensure that it works right is to uninstall crm 3.0, run the redeployment wizard mapping the users in the database to the users on the new domain, then reinstalling crm, pointing to the existing database.
I would call Microsoft support if I were you and have them walk me through their recommended steps. This will drastically reduce potential downtime.