Navy veteran opinion-
I dont know if this is posted yet, but this reeks to me of a discharge upgrade through the US Navy Board for Correction of Naval Records (BCNR).
This would account for the time delay, medal re-issues, and a bunch of Kerry's actions.
Yep. I thought so as well. Was looking into the navy reg:
http://usmilitary.about.com/gi/dynamic/offsite.htm?site=http://neds.nebt.daps.mil/Directives/5420174c.pdf
And it looks like that is what the paperwork in kerry's file is that he does not want anyone to see. They are applications to review his record and change his status.