Hey @Cyd @ich777 Thanks for the quick responses!
We have finally gotten it running. We had to boot the game in single player with the mods in for them to unpack, Then copy and paste them manually into the the mods folder on the ark-se of the server, Then we just added the ?GameModIds=x,x,x and it booted up and worked and loaded the mods.
No need to edit Game.ini or GUS.ini at all.
We haven't tested it with your path lines yet to run the automodmanager, But we will eventually we're just happy its' running now.