229, have you ever played a tabletop RPG about solving mysteries? Because you've said a few things that tie in with the principles behind those games, especially with how you plan to handle clues and evidence.
Dunno how much this fits, but it got me thinking of a few games. Ctuhulu Dark. It's a Lovecraft(Obviously) based game where when a play rolls a die? They're actions go well. They always go well.
The string attached is that if players want to see you fail, they can roll and who gets the highest result, gets to dictate what happens. The brilliance of this, is the sheer chaos and paranoia of it. Complete madness of what has happened, what didn't, and who, if, and when someone is going to suddenly try to screw you over.
Paranoia: The game is ran by a completely insane computer. Security clearances about what players can and can't do. It's a game where cheating is considered fine unless you get caught. The in game characters, don't know the rules and if proven that they do, will be executed. Example: Players can argue that something provides say that X thing lets do them Y action. However, players aren't supposed to know rules. Since they know that X thing would allow them to do Y action, they are therefore a cheater and die. If they haven't read the rules, they are not a cheater, but cannot do Y action, and die.
InSpectres: A supernatual/scifi mystery game. Success if rolled over 4, is determined by the player who narrates results. If less, by the Gm. There's also a stress mechanic about how players handle situations and a thing called Franchise Dice, which determine the pacing of the mission and how close they are to succeeding.
Anyway, those are just my random thoughts. I don't think much of these things could really be implemented in Chyoa format, without excessively using variables at every turn.