There are over 100 strains of HPV, some affect the feet, some affect the genitals, some affect the hands, etc. The ones that affect your feet won't ever affect the genitals, so this isn't an issue of cross contamination. The ones that affect your genitals won't affect your feet, either.
This could be warts, but warts don't cause the stinging sensation you describe, if that's associated with this.
Your recent sexual activity - how long ago was it? Was it your only time? I ask because genital warts have an incubation period (time of infection to the time you get symptoms) of at least a few months, usually longer. So if your recent sexual activity was maybe a week ago, and was your only activity ever, this wouldn't be genital warts. Does that make sense?
Lots and lots of things cause skin bumps, so definitely get it checked by your doctor. You might also want to show him the warts on your feet if they are persistent.
Let us know what happens. :)