I think it would be less messy (but also slower) if we required a 24-hour challenge period after each clue and disallowed retroactive challenges.
The whole mind game where you have to decide whether to say what you really clued in a challenge or make it line up with the guess seems like really bad game design to me, especially when you consider what it looks like to max points. It gives the cluer the power (assuming they can coordinate with the other challengee) to screw over their guesser even if their guesser guessed completely right, simply because the guesser is ahead on points.
I think the spirit of the game, as well as simplicity, would be better served if someone simply posted their guess and clue and then there were 24 hours for challenges, in which someone could challenge the clue. Then after that time expired the clue would be assumed to be consistent and anyone could make a guess. Or something. Do you all hear what I mean?