I think the problem you're facing is that you're an organic writer and you're trying to plot.
I don't plot anywhere except in my head. There are some things that I know should be in the story, and I know the general direction it's going in, but I don't plot.
Instead, I spend a lot of time working on my characters. I don't do this before I've written a thousand words or so, and then I'll stop and try to work out some basic things about the characters. I might do a lot of work on them or a little work depending on how well I think I understand them.
Basically I need to know what they want (the character's drive to attain this is the action of the story) and I need to know what they need (what they are lacking in their psychological makeup) - this can also impact upon the story.
Aside from that there are a lot of exercises I might do as I work on the characters, probably writing a bit and going back to the characters if I'm not sure where I'm going. Sometimes the characters take over (this sounds like the problem you're having). I'd say go with it, but ask yourself where the story is going to lead if you let the characters act the way they want to. Often, you'll find that the story will be better.
Ultimately, trust your subconscious. It knows what's happening.
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