I agree with Ewok85 about the polite usages.
Regarding onna no kotoba (words used by female Japanese) and otoko no kotoba (words used by male Japanese), kimi, boku, and ore are definitely not onna no kotoba. One particular onna no kotoba you will hear is Atashi.
Rare is the day that you will hear a Japanese guy say Watashi.
Yes, "Ogenki desu ka?" means "How are you?" By the way, genki refers to all aspects of emotional, spiritual, mental, and physical health, not just physical health.
Jessica, does that help?