1. 7 days per round.
2. Your example with Deflag is correct - no more than 6 total copies of Deflag across your 3 active decks in any round.
3. You may use each pillar or pendulum card in only one deck. Using Fire Pendulum in one deck bans it from your other two decks.
4. You may replace 1 deck at the end of each round. If you choose not to, that's ok too!
Thanks for the answers.
I suppose that the additional decks might have a pillar already used in the first 3 decks, but none of the set of 3 you are going to use must have a pillar in common.
That means that at the second round I can substitute my mono-dark with a duo dark-fire, provided that none of the other 2 decks I am going to use has neither Fire or Darkness pillars.
The same goes for the card counts. My 3 initial decks, for instance, have respectively 30, 36 and 34 cards (100 in total); if I decide to substitute the deck with 34 cards, I must make sure that the new entry has at least the same amount of cards to maintain the minimum amount of 100 cards.
Interesting rules. I think I will sign up! :-)