Thanks, John. I am glad that these details of my work are discussed, and not topics like "dude, there are not enough tits in your story!"...
"maybe you should warn the reader with a note at the beginning of the story"
There is nothing to warn about. I use quotation marks only for speech, irony or, well, quotations (I prefer double quotes, with single quotes inside of them if necessary. Some do it the other way round). The idea of the italic lines is to give the reader a clear indicator for the main character's thoughts without returning phrases (she thought, etc.). But this is only for the separate lines. Inside the normal text, italic is used to emphasise words or formulations, just like in every other narration, too. Thoughts inside the normal text are both italic and set in brackets (round brackets in US). I am aware that it somewhat dominates the style, but I do think it is worth it.
"Haven't gotten any complaints on that yet."
Me neither.I don't consider lucy's or your answer to be complains, but to be opinions of people who have taken their time to read my work -- and those opinions are always welcome.