Don't know if you're still working on this but I tried this today and got to the part where you start the server for the first time. Says it was supposed to create the Administrator.Arma3Profile and the Arma3.cfg files. Instead of doing that it created a whole new folder in Games\ArmA3\ folder called A2Master with AnimDataCache, BattleEye, and Users folders and arma3server_x64 RPT file and A3Master_4492 Text Document.
Have no idea what to do from this point. I did not edit the CONFIG_Vanilla.cfg file other than to change the name of the server and the adminpassword.