Thanks so much for the feedback and questions. I'm really intrigued by factions that don't battle, although it is a pain to make them work well while missing a core component of Root.
To answer your questions:
1. There is not a mechanical way - players just remember. It did cross my mind it could be an issue but in the few playtests I managed, it was usually clear as the Consulted Healer was in a clearing dominated by one faction. Plus I figured even if the Cabal player forgets who consulted who, the individual players wouldn't.
2. Once an Antidote is gained, it is a permanent buff for that player who can use it to cure any infected piece in a matching clearing. So the more Antidotes they gain, the more pieces they can cure at the start of each and every turn. In the Law of Root, I have added a suggestion to place your Antidotes along the Birdsong banner as a visual reminder.
3. When a Purify marker is used, the player who gained it places it in any clearing. All infection is removed from that clearing immediately and infection cannot spread there for the rest of the game. So potentially 4 of the 12 clearings will be unavailable to the Cabal player towards the end of the game.