This is the place to post questions and discussions on usage and style. The members of the Wordwizard Clubhouse will also often be able to help you to formulate that difficult letter.
1) I doubted the science fiction story I had written.
Does that sentence make sense?
The idea is that I had doubts about it; I didn't know if it was good or not.
The sentence seems fine to me.
Without any modifying context, I would assume that the speaker was principally questioning the plausibility of the plot (though it logically follows from that that the quality of the story overall must also suffer).