This article indicates that standalone servers can be stopped while performing these steps. One exception is step 15. If Portal is not running, you will see errors like this:
BUILD FAILED
C:\IBM\WebSphere\PortalServer\wcm\prereq.wcm\config\includes\prereq.wcm_cfg.xml:
3671: The following error occurred while executing this line:
C:\IBM\WebSphere\PortalServer\wcm\prereq.wcm\config\includes\prereq.wcm_cfg.xml:
3643: An exception occurred while executing the task: Connection refused: connect
To resolve this, start Portal and repeat step 15.
BUILD FAILED
C:\IBM\WebSphere\PortalServer\wcm\prereq.wcm\config\includes\prereq.wcm_cfg.xml:
3671: The following error occurred while executing this line:
C:\IBM\WebSphere\PortalServer\wcm\prereq.wcm\config\includes\prereq.wcm_cfg.xml:
3643: An exception occurred while executing the task: Connection refused: connect
To resolve this, start Portal and repeat step 15.