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I think you mean vim, which has syntax highlighting (or so I hear), not plain old vi.
My advice is not to worry too much about the program (they're all fine as long as they can export as HTML), and focus on the content instead. But if you wanna do it right, Adobe is considered the leader in desktop publishing. Get their Creative Suite and grab some tutorials from lynda.com. Of course, you can also talk to a publisher and they'll take care of it for you. But for a short story to put on your girlfriend's e-reader, any program is probably overkill.
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