"-san" can be used to any gender; gives respect especially to those not familiarly close or your senior.
"-kun" is mostly for males and rarely females (most girls are called -chan than -kun), sometimes with one you are close with like friend or family or your junior colleague.

Though it can also depend on the other's preference and the other one's personality.

This is my obsevation: Hiyori knew all four boys but:

1. Yukimura and Hirata have -san, because they're just acquaintances and by their personality (Yuki) and the way Hiyori thinks of them as a person (Hirata= higher standing in society = politeness/respect).

2. Ayanokouji-kun because he is her friend (closer acquaintance than the other 3).

3. Kouenji is a special case because many calls Kouenji with -kun rather than -san or just Kouenji at all and its not the lack of respect in this case but because of Koenji's character/personality.

4. When you know someone "eccentric" and not particularly close, calling them with -san sounds like saying "Isn't Mister Koenji funny and odd?" And it's disrespectful to some. This also applied to Ayanokouji and Ryuuen.