Not sure what you did wrong here. Mine went pretty smooth and here's what i did anyway

1. Activate the Preorder key from Square Enix store.
2. Entered the codes at https://preorder.na.finalfantasyxiv.com
3. After which it will show me the set of "Bonus Code" to be entered inside Mogstation
4. Login to Mogstation and entered "bonus code"
5. Voila, done. Just gotta wait till 19th June till the download is available.