When I started writing my YA Mystery SWIMMING ALONE, I actually wasn't sure who did it or why, or what exactly had happened. I just wrote and wrote... and eventually, I figured out my plot. Then I started to outline (and re-outline), and make sure all the correct clues were planted. The book went through a lot of rewrites! (Maybe if I had figured things out earlier, that would not have been the case!)
For me the key is that there is the actual solution, and then one or two other solutions that distract the protagonist. In SWIMMING ALONE, there is something really major that distracts her from figuring out what actually has happened. The book is in the first person, so I really tried to step inside her shoes-- what would she think if this happened. What conclusion would she draw?
But with my shorter mystery fiction, I worked much more organically. I usually know the ending (but not always) and write until I get there-- and then do a lot of rewriting to make sure the clues and red herrings are in place. And some of these stories aren't traditionally plotted at all.
I also think that with a mystery, what keeps it from being "boring" is the early "body drop." It doesn't need to be an actual body, of course, but then the reader will stay engaged as the character attempts to figure things out!