Ah, I remember back in the old days when you told me to try to simplify my works down. Not that I'm laughing at your predicament, just that I understand it.
Here's what I did with your advice all that time ago: I stopped worrying about the characters. Yeah, they're like my children and I wanted so much for them, but I had to shorten everything down, so instead of worrying about them, I focused instead on the things and events that I wanted to get done, and how to go about them as neatly as possible. Granted, I haven't done any solid writing in a long while, and I'm more than a little out of practice. Still, maybe that bit can help you out.
As for the third one, what's the dark secret, if I may ask? If it's something that can drive the plot, then it seems solid, but knowing the ways in which it will do so is more important than whatever it is, at least IMO.