Your questions are good ones. Before I address them, a few comments. You had as single exposure to a partner of unknown status. It appears from your history that you are likely to have gotten HPV (genital warts) from your exposure. As I suspect you are aware, HPV is the most commonly acquired STD. Over 85% of sexually active women will have HPV infection at some time in their lives. the figures are likely to be the same for men but there are less data. In some HPV will cause genital warts as appears to be the case for you, in others it will not cause warts but may lead to changes in PAP smears (for women) or no visible abnormalities at all (for men). In nearly everyone who gets HPV, warts or otherwise, the infections will resolve by themselves without therapy in 8-10 months. In a very small minority of women, HPV infection can persist and lead to the pre-cancerous lesions that PAP smears detect and which can then be treated. With this as background, let's got o your questions:
1. There is a form of leukoplakia called "hairy leukoplakia" which is HPV related. Leukoplakia however is a non-specific term and if you had hairy leukoplakia I suspect the report would have said so. This being the case, my guess is that your leukoplakia and your sexually exposure 8 months ago are unrelated. My advice would be just to have your dermatologist follow the leukoplakia.
2. HPV typically does not cause symptoms and it is unheard of for HPV infection to cause fever, lymph node swelling and muscle aches. My guess is that you had a flu-like illness unrelated to the exposure you describe.
3. Most HPV treatments have similar response rates and, unfortunately in about 20% of persons after initial resolution, they can recur. That your warts have appeared recently increase the probability that you will have a good response to therapy, irrespective of which one you choose. I don't have a favorite therapy. The laser and CO2 therapies can be applied by your doctor and may require return visits to complete the therapy. Aldara has the advantage of being self-administered. I know little about photodynamic therapy.
For addition information on this most common of STDs, I would suggest search for other HPV- and wart-related Q&A on this site, as well seeking addition information on sites such as the American Social health Association web-site (disclosure, Dr. Handsfield and I are both on the Board of ASHA)..
Hope this helps. EWH