So I think the main goal of the ruleset should be to be playable with only two people, without a "referee" or "helper". So this is not really a hidden move go, but a close alternative. This is what I think achieves that:
1.The players agree on the number of hidden moves.
2. They decide on the moves and submit them to the Malkovich log unambiguously. e.g.:(HIDDEN MOVES: C3, Q16, R3)
3. They start the game.
4. Each player has to keep track if their hidden stones are alive. If they die, it should be submitted to the Malkovich log (to make keeping track of the game easier, e.g.: DEAD HIDDEN STONE: A2), and they are like they never existed. The opponent should only be told about the death if it affects other stones or a ko, then the hidden move should be played with one pass from the opponent to get it on the board.(this should be told in the chat e.g.:HIDDEN STONE DIED: A19)
5. If your opponent plays a stone on a hidden move of yours which is alive, you sign it in the chat (e.g.:HIDDEN MOVE: C2), he/she undoes his/her last move, you place your hidden stone, then he/she continues the game.
6. Before one's move he/she has the choice to announce in the chat one or more hidden move (e.g.:HIDDEN MOVES: G8, H9) which are put on the board while the opponent is passing. Then one can play the stone which is not a hidden one. It's illegal to use hidden moves as ko-breakers, if the not-hidden move would have been an illegal ko, it will be illegal after the placing of the hidden stones as well.
7. If your opponent announces a hidden move which is a hidden move for you as well, you have to announce this in the chat (e.g.:DUPLICATE HIDDEN MOVE:J10), and none of the players can place the hidden move. Of course the player who announced the move originally can use his/her turn to place a stone there.
8. At the end of the game it is easy to check if everything was in order using the chat and the Malkovich log.