Those problems--and many others--usually mean I don't actually know what my story is. I have characters I like, a tone I like, a theme I like, a situation I like, a general shape I like and/or an ending I want, but I haven't dug into all those things I like and defined the story.
That's because defining the story means removing a lot of what I like. I want to say this, I want to say that, I want to explore this setting or that emotion, but I want to write a short story. Well, a short story only has room for so much. If you want to present more than a short story is capable of carrying, you have to write a novel--or a poem.
Jim Butcher calls defining the story coming up with a story skeleton or story question. In his definitive LiveJournal postings, which I highly recommend, he says:
The story skeleton (also called a story question) consists of a simple format:
*WHEN SOMETHING HAPPENS*, *YOUR PROTAGONIST* *PURSUES A GOAL*. But will he succeed when *ANTAGONIST PROVIDES OPPOSITION*?
"Antagonist" can mean someone else, a goal that's counter to the goal he's pursuing, circumstances or whatever:
When the ghost of his dead partner shows up on Christmas Eve, moneylender Ebenezer Scrooge just wants to be left alone to continue his miserly life as it is. But will he succeed when he's forced to relive his past, view the present, and foresee the future?
Another way to find your story is to pretend it's already written and you're writing to an agent. You have one paragraph to grab the agent's attention. Kathryn Craft, a developmental editor at Writing-Partner.com had a wonderful post about this on The Blood-Red Pencil, a fantastic blog for writers and editors which I also highly recommend. She says, among other things:
The pitch is a 2-3 sentence summary that includes the “who, what, why, and why not.” Just enough information to intrigue the agent (I want to read that book!) and induce salivation (I think I can sell that book!).
You can structure the pitch any way you want, but you can’t go wrong with the following formula: When [A] happens, [B] wants [C] because [D], but [E] must first be overcome before [F].
A = inciting incident
B = protagonist
C = desire that drives the book
D = motivation of main character
E = obstacle/conflict
F = ending
To get the most out of your pitch, layer the A-to-F formula with
descriptors that imply the genre.
When a dark power overshadows Middle Earth, Frodo Baggins, a mild young Hobbit, is determined to defeat it or die trying. Though the destinies of many races hang in the balance, it's love of the ordinary peace and plenty of his native Shire that gives him his courage, and the loyalty of his Hobbit companions that sustain him in his journey. Although the Dark Lord sends legions and monsters, creatures and corruption against him, a small person's willingness to sacrifice self for the good of others is stronger than anything the Enemy can do.
You could probably come up with better ones. Try to. Pick a book or movie you feel is particularly strong and try to write a story skeleton or pitch summary for it. Do several for practice. Then do it for your own work-in-progress and see how that goes.