Much of the information you gave in the first paragraph is far too advanced and too much medical jargon for me. I would suggest having your doctor explain this to you.
If you had warts many, many years ago and haven't had a recurrence since, chances are this has absolutely nothing to do with genital warts. HPV infection is not permanently contagious and symptomatic, eventually the body's immune system beats it- usually within an average of 8 months. Also, genital warts are in no way cancerous. The type of HPV which cause cancer are high risk strains and do not cause genital warts. The strains that cause genital warts are low risk strains, which don't lead to cancer. I would keep seeing a gynecologist, but if you do not trust this one, see another. You HAD HPV, but I would say you're "cured" (see Dr. HHH's information about this concept in the expert forums).
If you can't discuss this with your doctor, I'd suggest paying the $15 and posting in the expert forum (regarding your cyst). But I wouldn't worry about HPV at all in this case, personally. This is just my two cents though, and I'm not an expert. If you are worried, seek a second opinion.