When a story is finished and there are parts that just aren't working, sometimes magic is required. A dab of this here and a dab of that there, say a little prayer and presto...the story changes into something completely new.
I've been working this brand of sorcery on one my recently completed stories. After carefully considering what elements were strong and which were dragging me down, I kept the good bits and rethought the story into one that plays better with the narrative. A few characters survived in tact while many more suffered through excruciating transformations. Either way, they've been cooperative so far.
This is a process I've gone through with nearly every novel I've ever published. I'm sure there has to be an easy way...but part of being a writer is finding the path that works for you.