It was pointed out that Notes uses the Firefox engine so I was able to do investigation of getting Firefox to work with IWA and once I had that I would have Notes working!
In Win 2012 R2 ADFS doesn't use the IIS interface at all so there is no way through the interface to turn off Extended Authentication. You need to do this through PowerShell (Which I had already done). Additionally there is another ADFS property that needs to be set so that the Notes client can authenticate using IWA the commands are below (This is what I didn't know and what made it work):
Disable extended token authentication:
Set-ADFSProperties –ExtendedProtectionTokenCheck None
This one determines what browser agents can use IWA. Note that Firefox/Mozilla are not on the list by default and since that is what Notes uses you are out of luck unless you update it. Add any other user agents that you want to use IWA. Find the exact names in your domlog.nsf or weblogs.
Set-AdfsProperties -WIASupportedUserAgents ("MSIE 6.0", "MSIE 7.0", "MSIE 8.0", "MSIE 9.0", "MSIE 10.0", "Trident/7.0", "MSIPC", "Windows Rights Management Client", "Firefox/25.0", "Mozilla/4.0", "Mozilla/5.0")