I'm currently using Win-Acme to refresh/renew certificates.
However I currently have to run this every month manual because it cannot run via the Windows Sheduler since it will require Administrative permission.
Are there any other ways to do this or extend the time that a SSL certificate is valid to more then 90 days so I don't have to run this tool so often ?
This sounds like your problem--either get administrative permissions, or come up with some other way to run this on a schedule. Or use a different client.