As you used your Dynamics CRM 4.0 database you may have had occasion to add "unsupported" objects to the database. These could be anything from indexes ( fairly supported ) to triggers ( pretty unsupported ) to custom stored procedures.
You need to consider removing all of these additions prior to the upgrade.
The pre-upgrade validation checks will give you a warning that unsupported things exist and the installation may actually fail, depending on the changes you made. And as noted by an article, item #3, from Customer Effective, the error message may not be very clear as to what the problem is.
Just a word of warning.