If ever a story needed an outline, it would be the mystery story. While most fiction can be written successfully by the seat of your pants, so much is happening in the background of your average mystery novel that you will forget things without an outline. Write out your plot first, or at least before going beyond your first chapter.
Once you have your outline, read it in reverse. Think, with each discovery: does this make sense with what comes before it? You will find forgotten clues, better clues and gaping plot holes. Make your corrections as you read backward through your outline.
Pacing is of critical importance in a mystery story. Mark points in your story where your main character finds clues. Keep those points close enough to maintain high reader interest, yet far enough apart that you can tell your story and have subplots in-between. This is a difficult balance and takes practice. If you have trouble with it, pick up a good book on how to plot well, like "The Marshall Plan for Writing Fiction" or "Writing the Novel" by Lawrence Block.
Read great mystery novels by Sir Arthur Conan Doyle, Agatha Christie, and Ellery Queen, and mark them up. Use a bright-colored highlighter and on every page with an important clue or turning point in the story, color the upper corner of the page, so that you can see it when you close the book. Once you're finished with two or three, look at the colored edges with the book closed. You'll start noticing a pattern: ten or fifteen pages of story, then suddenly a clue. This is how often your own story needs to plot in clues and turning points. Try this same method with outlines of classic mystery novels. Do not do this exercise until after you've written out your own plot outline. That way, you won't be so worried about the plot point pattern that you forget to tell the story.