We're a few days in to the game being back online and things are looking good so far. There are a few outstanding in-game issues, like flags and sails not appearing properly, and we will get them fixed as soon as we can.
Hamled is working on getting the Burning Sea Note store up and running, and estimates that it will be done early next week (again, barring interference from dreaded unknowns). After that he will be getting registration working again. We are also working on a solution for players who no longer have access to the email address their account was registered to.
Thank you all for sticking with us through this, we're working on getting everything working again and appreciate your patience while we bring all of PotBS's systems back online.
EDIT: I forgot to mention this, but I've seen a number of people ask about Physx issues. You can find the version of Physx required by PotBS at http://www.nvidia.com/object/physx-9.12.1031-legacy-driver.html.