Running Mysteries and Investigations in L5R
Running mysteries in L5R is a big shift from running mysteries in other settings. You shouldn't think of the challenge of the mystery to be "figuring out what happened", the focus of the challenge should be "We figured out what happened. Now what the hell do we do about it?" Make getting the clues easy, and reward smart lines of inquiry from the players. Make acting on the clues the tricky part, and use that to thrust the PCs into dramatic situations.
Example: the testimony of the spirits say that Bayushi Bob did the murder. So now they have a pretty good idea who did it, but they now have to DO something about it to pin it to him.
Do they go to Bayushi Bob and pressure him into confessing?
Do they go to his lord and try to pressure him to give up Bayushi Bob and throw him under the bus?
Do they go to a trusted ally and ask that they give false testimony, so they can at least stick it to him?
Do they plan on goading Bayushi Bob into a duel so they can prove themselves right with the skill of their sword?
Those are the parts of a Rokugan mystery that keep it interesting. Finding out what happened in the mystery should be the easy part. DOING something about it and resolving it should be the truly challenging part.
This keeps the adventure in the hands of the players, rather than them just piecing together what an NPC already did. The forensics of the mystery should only be the first half of the Law & Order episode, the second half is where the game happens.