Patching Plotholes

Does your story ever feel like this?

I look at this picture and I think, wow, now that's a lot of potholes. Of course, this is a dirt road, so maybe that's to be expected. However, the poor sucker who has to fix these potholes has quite a job cut out for him. I kind of feel that way right now about my espionage fantasy.

And you can only work on plotholes one at a time.

In order to repair a pothole, sometimes it's necessary to bring in some heavy equipment. And sometimes, that heavy equipment causes new potholes to form. I'm dealing with this as well. "Ok, so I've rewritten the entire catalyst scene from scratch, but now I have a dangling plotline where this didn't happen the way it did in the old scene, and at least ten or fifteen scenes further on down the line absolutely depends on this happening."

If I'm not careful, I'll be repairing this thing forever, and when it's finished, the patch will look like this:

when it needs to look like this: