In order to create custom notification job, powershell script (attached) should be ran on the App server.

Before running it client needs to specify following values for the variables in the script:

1. $file - path to the notification template location (by default pth leads to the Shareknowledge Default Notification library on th eAdministration site.) For each timer job there should be individual template file uploaded to the library.
2. $schedule - this value could be left by default and modified afterwards in the Central Administration ui or desired value could be specified in case the client knows it beforehand. Registered values for the schedule could be found here:
https://technet.microsoft.com/en-us/library/ff607916.aspx
3. $sitecollectionurl - ShareKnowledge site URL
4. $appserverurl - the name of the APP server as it is seen on the 'Manage servers in the farm' page of the Central Administration

Additionally current version of the ShareKnowledge should be specified in the lower part of the script in case it differs. Placeholder -  'Version=4.6.4.0'

In case of need to delete created Timer Job $onlyDelete variable value should be changed to $true

CustomSKNotificationTimerJob.zip