I'll give a full explanation of what happened, to those who think a replay would be feasible.
G1 - Won with Phoenix NM against Fractal Chargers.
G2 - Lost with Rage Angels against Fractal Retros
G3 - Won with Grabbow against Sanctuary Stall
G4 - Won with Rage Angels against Light Stall
From deuce's perspective, the Light Stall was a weak choice in hindsight, but it wouldn't cost him the match, because he wouldn't have to play it again.
From my perspective, I simply needed to beat his Light Stall with all four of my remaining decks, and I'd win the match.
Thus, I built 3 Firestalls (with Reflective) and 1 Fractix (with 4 Deflags) to hard counter deuce's Light Stall. Unless he had Fractal+Dragons in his sideboard, it was nearly impossible for deuce's Light Stall to win against these 4 decks. Even if I lost the next 5 games against his other decks, all I had to do was to not let his Light Stall beat me. That is the nature of Conquest. If you have a single deck that cannot win a game, then you lose the entire match.
Which meant that playing a Light Stall was incredibly risky. Even though it's a good deck, it's easy to hard counter, which is what you have to avoid if your opponent still has most of their decks unrevealed. If deuce had known the rules from the start, he wouldn't have played the Light Stall at all, and I wouldn't have built 4 counters to it in response. deuce's strategy would have been drastically different if he had known the rules, and my strategy would have been drastically different in response. Thus, there's no simple solution to this. Even if the match was replayed from 0-0, we would know what sorts of decks our opponent has prepared, which would kill the fun. The only solution I can think of would be to replay the match at 0-0 with drastically different rules, and neither of us want that.
I suppose the moral of the story is to double-check the rules, and don't use the Conquest format if players don't have to submit all of their decks before the first game.