If you're anything like me, you write best when you're aiming for a high point—the climax of the story, hopefully—or else a series of high points. If you've got "whodunnit" in the mix, the Big Scene is probably going to be the revelation of whodunnit (or whatdunnit, with horror) and how much danger the protagonist gets into from discovering that. My advice would be to take a careful inventory of what you need to take you to your Big Scene. If you make sure all those elements are in place, then I think everything else will fall in line.
Hopefully. Maybe. If not, at least you'll have a more coherent idea of what in particular is not working.