Hey Tybalt, that really sucks and I understand how you feel. I went to a "prestigious" school for my undergrad and we were told that anything under a 3.7 gets tossed into the "maybe" pile by the MA adcom at that school. However, you have a 4.0 in your master's plus excellent credentials which should assure them as to the high quality of your work. Don't give up hope - the master's grades are just as important, especially in cases where significant time has elapsed between the two. And I agree that your personal problems during the undergrad should be addressed (briefly) in the app, so don't sweat it. I would've definitely done the same; after all, many departments explicitly say you should take the time to explain any perceived shortcomings in your application.
Good luck! I am crossing my fingers for you.