I'm in the same boat. My account was NA during FFXI, but I am now in Australia, and that is EU (heavens knows why).
When I got my pre-order redemption code it told me "Please note you will need a Square Enix Account to redeem these codes. If you do not already have one, please go here to register: account.square-enix.com".
It allowed me to enter my code during beta 4, and then showed I had FFXIV:ARR on my account.
But when I received my physical Collectors Edition copy, it told me "Code needs to be the same as region" (or some such thing).
Emailed support, no reply. Sat up all night one night with Live Help doing the same as you....1st in line, then they cancelled. Finally spoke to EU Live Help that pretty much told me I'm **** out of luck.
Two choices. make a new EU account, lose my characters, lose my pre-order items, and not be able to make a character to play with my son and my partner. Or buy another downloadable Collectors Edition and apply that to my NA account....problem there is that SE is no longer selling downloadable copies, and Amazon will not sell outside USA.

That a PC game is region locked is ridiculous, and that they will not do a region transfer is just as ridiculous.
Five days spent trying to figure a way to register a game to my account and play and I'm still no closer. And deadline is almost on us.