We have user VPN setup and working tied to AD. Unfortunately I am having hell getting it to work with DUO. It seems the request is never sent to the DUO side based on what I can tell.
Are there any issues with have the DUO proxy service installed on the same server that hosts NPS and Active Directory (single DC environment for the moment).
You can change the listening port in DUO auth proxy config to a different port than the default radius ports of 1812 and 1813. Then set the radius port in the Fortigate radius server config to point to the new port. Make sure that the new port is open in the windows firewall.
We never could get it working on our HA pairs at the same time. We had to switch everyone to Duo and remove the ldap groups and config all together. I believe it is supposed to work with either at the same time but I failed to find much documentation to support that.