You need to be really sure you want to split into two Orgs before you go down this route. This would mean the customisations for the two areas would be completely separate (which you may want), and users will simply not have any access to records from the
other org (although a user may have a log on to both, they can't for example relate an Opportunity in one Org to an Account in the other.
Back up your database and import into SQL twice. Import into CRM 2011 as a new Org and let the upgrade do it's work. Then disable and delete the org from 2011. Then import the second database to upgrade it. Now re-import the first one again (if you don't
do this, the second one will refuse to import as it sees the GUID is already there from the first one).
Use the bulk delete tools in CRM 2011 post-upgrade, you will probably find this easier than in CRM 4.
Data does not really 'belong' to business units, it is owned by users who are in BUs.
So create a query to find (for example) All Accounts where the owner is any user who is in the BU you are getting rid of. Delete these records and you should find it also deletes many of the child records. You need to check all your relationship types, as
some may be set to prevent the deletion of a parent when there are child records below it. Repeat for Contacts, Leads, Opportunities, etc until you are happy.
Then in Org 2, delete the other half of the data.
Disable users in Org1 and Org 2 as appropriate.
Hope this helps. Adam Vero, MCT