Writing Out of Order

My preferred way to write lately has been to write out of chronological order. I’ve been jotting down whatever short scenes pop into my head.
It’s proved useful (if mildly confusing) because I tend to have blind spots when looking at how my plot will turn out. I may know what happens next, but I don't know how or why it happened. In other words, I'm missing a few stepping stones.

I’m now attempting to type up what I’ve got so far, trying to figure out how to fill the holes.
I couldn’t really gain any semblance of organization, so I filled out index cards with a short description of each scene and arranged them chronologically.
What resulted was a clear definition of what I need to type. But it also revealed that the skeletal structure of the plot is terribly frail. But that's alright, for a rough draft.

On several of them, I state the scene but then have scribbled how? underneath. I know what happens. But I can't figure HOW. For example, I know they escape from ______ but I don't know how they accomplish that.