Friction (and podofilox) can cause irritation, which in turn can lead to extra pigmentation. However, if it were just discoloration, you shouldn't be having pain. I don't think you have an STD, but I think you need to be seen by a doctor. That shouldn't take months. Meantime, avoid friction and apply nothing stronger than vaseline.
By the way, getting warts a week after the kind of contact you describe sounds coincidental.
Take care.
Dr. Rockoff