There is no mechansim that I'm aware of to automate the cloning of users (user accounts and associated credentials) to another machine other than to use the restore from backup process.
Local user passwords are stored in an encrypted manner on the system. Note that LDAP user credentials are not stored by the system; the same is true when SAML SSO is being used.
Stored passwords that are used by users within a data flow (e.g. for accessing a DB, Salesforce, etc) are stored in a local Java Key Store (.jks file) as described in the restore from backup process.This could be manually transfered from a source system to a target system (and is performed during the backup from restore process.
A user's data flows and custom library nodes can be exported (individually or en-bloc for all data flows in a partcular directory). The resulting .lxa can be imported into the corresponding directory on the target system. An admin user can access the data flows of other users via the 'All Folders' tab of the directory view.
User files that have been uploaded to the source system, and files created by users when data flows are run, are stored in the sub-directories of the shared data dirctory (as specified by the ls.lae.shareRootDir property in the cust.prop file). These would need to be copied to the target system.
It is not possible to export schedules or Run Property Sets so these would need to be manually recreated on the target system.
Importing data flows creates a new instance of the data flow on the target system so there is no state information the data flow (since at this point, the data flow has never been run on the system). Hence there is little point in transferring the temp data directory from the source system when the restore from backup process is not being used.
Any changes made to the source system's 'site' directory (e.g. any JDBC drivers added to the system or modifications to configuration files) should be recreated on the target system's 'site' directory.
Because of the limitations of attempting to clone a system using a manual approach, the recommended mechanism to ensure all aspects of a source system are recreated on a different system is to use the resore from backup process.