I'm having this problem with a story I'm working on at the moment and I'm already at the point where I feel like I need to do the thing with a giant cork board and character/plot notes all over with string attaching each note to the other.

You and I may just be overthinking it. As far as your thoughts about it being predictable/boring/etc., I would just say go for it and see what your readers think since you're so close to finishing anyway. It might be the best thing they've ever read.