1) If you lose your match, you are allowed to revert your deck back to the way it started for the round. If you lose the match 0-3, you may remake your deck, excluding the cards you made your previous deck with 9 (excluding marks, pillars, and pends)
Sounds good though I'd go a different way here.
If you lose 3-0, either you got countered or your deck simply fails. If you got countered, there is no need to change your deck anyway, maybe your deck is a counter to the next opponent? But if your deck fails, I'd say it is allowed to go back to any completed mark and build any deck there. You will lose one round since you have to re-complete your mark, that's the penalty for building a fail deck. With this rule, you don't need to play that fail deck, but are able to keep playing with a previously finished mark.
You will have to build your new deck before the matchups are set (maybe ask the organizer for a little additional time here).
2) If you are the recipient of a bye, you have a random mark completed (Including the one you are currently on).
Well, what happens when you randomly finish the mark you are currently on forces you to use another mark, so your deck becomes unplayable?
I'd still say that a bye reciever gets a ranom mark completed, excluding the one currently on. If the current mark is the last one to be completed, you won't get it completed, except someone else completed all marks in a totally legal way, so they can have a match to decide the champion.
3) If you face an opponent that has been given a bye, you are allowed to remake your deck, keeping your currently designated mark.
This might be a problem.
When matchups are set and you see who your opponent is you can simply build a counter to that deck. Making it impossible for someone who got a bye to win next round.