Well this may be a battle you will not be able to win ... you should have NOT filed the return before you got the SS#. If you put the return on extension you had 6 months to file the return so why did you file it early ? If you did not electronically file the extension then you may never change the IRS's position on when the SS# was issued.
As I recall from an IRS forum I attended that once you file the return it "closes" the extension on that tax year so you probably should have waited to file the return ... now you may need to amend the return to put back everything the IRS disallowed and send enough proof that your argument is sound. Of course this will take 6 months to a year (maybe longer) to play out ... good luck.
