This was much longer but there in the end.
Instructions:
Download the zip, and extract it. Go in it, and copy the folder there (it weirdly put it in another folder, sorry, don't know why), into the XMLMods folder in your AI War 2 directory.
Once it's in there, go to PlayerData, in the same directory, and open XMLLoadingOrder.
Under _Vanilla, put "ArkTest" (remove the quotes).
Should now be able to upgrade Arks as before.
Should note that you'd want to take these out once the new update hits, as this'd override that. Just remove the line from XMLLoadingOrder, and the folder from XMLMods.