Re: plotting a mystery. I don’t plot ahead or outline. I rarely know who done it until I’m at least two-thirds or three-quarters of the way through the manuscript. But I do have a plan.
By the time I need to know who done it, every character has a secret or two to hide, everyone, just about, has a motive, and most of them the opportunity, and some of them the ability (strength, or marksmanship, and so on) to commit the crime. And there are a few clues that could point to any of them. Those clues that don’t finally point to the killer are the red herrings.
Easier than going back and putting stuff in. It should almost all be right there. Then you can pick the suspect you believe it will be hardest for the reader to guess.
Piece of cake. Right? Well, maybe not, but it’s a start.
However, if you’ve already finished the book and discover you didn’t hide the villain well enough, I suggest going back and taking three or four other characters, give them each a motive and a clue or two that leads to them, and have your protag eliminate them one by one. Then go through the manuscript on screen, search for each character’s name, and read through each scene he or she is in to be sure it all holds together.
Then have another piece of cake.