I find using an illegal deck since round one a major problem. Anyone who uses an illegal deck, whether they'd win or not the match with the legal one, should lose the match. And as you have been using it since the first/second round, you lost right there.
That's, of course, my opinion that you shouldn't receive your code. It's an illegal deck all over the tournament, and people who used a legal deck (or not?) get a third and fourth award?
I, for one, am of the voting that you shouldn't have received second place or any code. But I guess that happened, right?
What didn't happen is that using an illegal deck all tournament long is a major disruption of the tournament when it's discovered, and it is quite the failure to read the rules in the thread. I would assume a one-week tournament ban would be issued out of this, according to Tournament Rules...