1) There's probably nothing anyone can do about your gil in the free company chest until someone with access logs into the game and can get it for you. Sorry, but that's just a tough break.

2) At this point it's probably too late to enter a valid early access code to get the early access bonus items. Contact square support, in-game GM's can't do anything about that administrative stuff. I think this is the link you want for that: https://support.na.square-enix.com/c...p?id=5382&la=1
I got to there by following "Support" links from the Mog Station.

3) I think you can upgrade to Collector's Edition at any time? If that's the case and you have a valid CE code then see if there's a way to register that code to your account through the Mog Station and you may still get the Griffin mount + Baron Helm + Wind-up Kain. If you can't then use the same link above and contact support.