Hi there. Wolfie´s got it right. I´m just gonna add a few things. In Japanese schools they often use "(a family name)-san" for a girl, and "(a family name)-kun" for a boy. Now, although we are accostomed to use "-san" for a grown-up woman when we are not very close to her, "-kun" can also be employed for a woman when a superior (in the job) talks to her, either with her first or family name. This happens because "-san" sounds more respectful. Hope this could be a help.

Okay. I got this one. -kun and -san are both honorifics and you seem to know how to use them. However, they have very different connotations to them. "-kun" is for someone you are familiar with, like a friend; you are older than them; or higher up in status than they are. This honorific is used only for a boy, though. The girl equivalent is "-chan." So whoever is calling Naruto "Naruto-kun" is most likely a friend. "-san" is the English equivalent of "Mr.", "Mrs.", or "Ms.". Whoever is saying this probably does not know Naruto very well. Or they are just showing respect because they are younger. I think that covers it, but if I need to clear things up, feel free to ask.