Installation has changed if the Modding Forums are to be believed, you only need to use commandline to install/use a custom map, makes sense why it's working for me without it.

MOD ID --> 479295136 <-- You will see a folder and 479295136.mod file
If you don't have both steam is acting up again, delete the \Mods\ folder and reload steam

Step 1: Sub to the mod, load singleplayer, this installs the falls into your steam folder

Step 2: Find your Steam\steamapps\common\Ark\ShooterGame\Content\Mods\ Folder
Close ark && steam and zip this folder up. (if your dedi server supports unzipping, if not upload 226mb one file at a time, if you don't know how to ftp/upload contact your provider)

Step 3: Find the ShooterGame\Content\ folder and create a Mods\ folder in there
Then upload the zip file into that folder, or all the files one at a time uncompressed @.@

Step 4: Go into GameUserSettings.ini find [ServerSettings] and on the very next line add
ActiveMods=479295136 (If you want to stack mods add a -> ,modid <- per mod you want to stack, it's important what order you stack because some mods are dirty and tamper with core.

**** I can't help you with stack order, I honestly only use my own mod ****

Step 5: Start your server and test
Press escape and see if it says Mod: Aku Shima
Test if the engrams are in your engram list (bery end, as this mod doesn't tamper with files)
You will need to enablecheats serverPassword
Test if you can spawn an item in --> cheat giveitemnum 405 1 0 false
Test if you can place the item down.

If you get a mod mismatch error, steam didn't download everything properly, delete your Steam\steamapps\common\Ark\ShooterGame\Content\Mods folder and restart steam and load singleplayer again, and reupload the files.

If you can't spawn the item, and they are in your engram list, the server doesn't know the mod is installed, make sure you added ActiveMods=479295136 under [ServerSettings] and saved the file while the server was off.

Also make sure to edit the right one.
WindowsServer -- > ShooterGame\Saved\Config\WindowsServer\GameUserSettings.ini
LinuxServer --> ShooterGame\Saved\Config\LinuxServer\GameUserSettings.ini

Starting your own non dedi server.

Windows:
ShooterGameServer.exe TheIsland?listen? TheIsland?listen?SessionName=<ServerName>?ServerAdminPassword=<ServerPassword>?multihome=<ServerIP>?Port=<ServerPort>?QueryPort=<SteamPortYouUseToConnect>?listen -server -log

Linux:
./ShooterGameServer TheIsland?listen?SessionName=<ServerName>?ServerAdminPassword=<ServerPassword>?multihome=<ServerIP>?Port=<ServerPort>?QueryPort=<SteamPortYouUseToConnect>?listen -server -log

Ark.Gamepedia dedi server help (linux)
http://ark.gamepedia.com/Dedicated_Server_Setup

Ark.Gamepedia rented windows help
http://ark.gamepedia.com/Unofficial_Server_Hosting_Guide