My original post left out too many details, below is timeline that will better explain the timing, my actions and the responses of SE support. I will also list everything I lost because it will help to explain why I am trying so hard to get a full restore.
Where my account was before the hack: Large House, +5 million Gill, All classes/jobs at lvl50, PLD & DRG with ilvl130 gear and zeta weapons. All the other jobs had ilvl gear >120 and their Zodiac weapons were >Animus, all the Disciples of the Land and Hand were fully equipped with the maximum over-melds, max gear and Lucius tools.
Once piece of info: This hack was done by someone I know. They were able to delete my toon because they had access to my cell and computer while I was out of the country (I don’t take my phone with me on international travel because of theft). (When I got back, my computer, phone, Facebook, twitter, Steam, Xbox Live, etc... were all deleted. Luckily they couldn't get access to my backups, so I wasn't complete screwed)

May 1st 2015: Last login before I went on vacation
May 1st~14th: Sometime while on vacation my account was hacked
May 16th: Discovered my toon was deleted
May 16th: I filled out compromised account form
June 1st: I received no response to first compromised account submission so I filled out the form a second time.
June 10th: Called support to find out the status on my recovery. Support informed me that they have no way to see the status of the ticket nor can they contact the restore team in Japan. They then directed me to fill out the form a 3rd time.
June 19th: Received an e-mail that my character was restored and that I am no longer eligible for another restore. I am unable to login because of the servers are down while being upgraded for the expansion.
June 20st: Login to the game to find out that my toon was restored to a point from over a year ago. Based on the gear and items in my possession, I they restored it to May 1, 2014 instead of 2015.
June 20st: Created ticket explaining that the restore was botched and that parts of the game are now locked with no way to unlock them.
June 22nd: Received email stating: "Unfortunately the SQUARE ENIX Support Center cannot assist with this issue via email. In order to further assist you, we will need you to contact us via phone or chat.."
June 22nd: Called phone support, they said they have no access to change anything in game, but that the GM's can fix it and that I should contact them to request a "character restore".
June 23nd. Contacted the GM's; explained my situation and stated that the email/phone support tech directed to contact them and request a "character restore"
June 23nd: I received a template response: "We have reviewed the details you have provided and determined that your concern can best be handled by the support Center team. In order to open a ticket....." Creating a ticked from the link they sent is how I got to this point to begin with.
June 24th: Created a new ticket explaining my situation again.
June 27th: Received an e-mail stating “Regarding your request for account support. Please find your answer below. If you discover a bug in the game, please create a thread containing the details of the bug in the 'In-Game Bugs' section in the 'Support' forums of the FINAL FANTASY XIV: A Realm Reborn Forums." " I did create this bug report even though this isn't a bug and they don't reply or address individual or address.
June 27th: Called Support: Explained everything that led me to this point (previous tickets, GM's...). I was told that "If your account was restored after it was compromised , then it was restored to the point at which it was last accessed appropriately". (This is definitely not true; I know my account had not been accessed by anyone except me during this time period.) The tech said that they don't have the ability to do anything in-game and that I should try contacting the GM's again and create a bug report.
June 27th: Contacted the GM's a second time. I relayed to them the name of the SE support Tech and his exact instructions for getting my account restored.
June 27th: GM’s template reply: “Users cannot restore deleted characters themselves. If you would like to request a character restoration, please fill out the below form, and we will analyze your situation to determine if support is possible.” The link is to the “Compromised Account: Support Form”
June 27th: Filled out the Compromised Account Form and submitted it. I have since filled it out 2 more times, once in the middle of July and again last week. I still haven’t received a response to any of them.
This cycle was repeated again in my attempt to get my account restore to the way it was before being compromised. I then repeated it two more times, the third time was when I tried to get SE to restore the missing soul crystals and the fourth was to reset the job quests for the soul crystals so that I could reacquire them.