Custom User Mapping

I have a scenerio where I need to migrate a specific list of users from the source domain to existing user accounts in the target domain.  At this time I only need to sync the user accounts so all of the source domain groups the user is a member of are created in the target domain and the target user is added to those groups.  I am having a hard time figuring out how to implement this scenerio.

Constraints:
- Users are in multiple OU's in the source domain comingled with users that should not be migrated, ldap filter cannot be applied.
- Groups are in multiple OU's in the source domain comingled with groups that should not be migrated,  ldap filter cannot be applied..
- There is no matching user attributes between source and target currently, though an attribute could be added to the user attributes in the target domain.

I was hoping a custom user file could be imported that matched specific source attribute to specific target attribute. The hope was that this file would limit the scope to the users synced and only the groups the users are members of including the parent groups.

Does the tool support this solution? 
- If not, is my only option to segregate all source users into a specifc OU(s) that are not comingled with other user accounts?
- Will the tool on sync only accounts and groups based the matching attribute from the source that can be applied target users that have been identified?