doc: add the --run command for manual job execution
    
    A manual method was mentioned with no specificity. Include
    the --run command. Also update the troubleshooting section
    to show what failure to restart the CA after configuration
    looks like.
    
    Import the IPA CA chain for manual execution.
    
    Also fix up some $ -> # to indicate root is needed.
    
    Related: https://pagure.io/freeipa/issue/9294
    
    Signed-off-by: Rob Crittenden <rcritten@redhat.com>
    Reviewed-By: Florence Blanc-Renaud <flo@redhat.com>