As far as your question in regards to sex reassignment. Sadly it doesn't go away when you change genders. It's within your body, as a virus. So it'll be there if you went from one gender to another sadly.
Hi,
In general, from what I understand regarding genital warts(HPV), the warts can reappear even after being treated, because the virus goes on living within your body, although you may not show any signs. It's also possible to pass the virus on to others that you are sexually active with.
In regard to your question about bottom surgery; you should probably ask a doctor or medical specialist about the use of genital tissue. There are sites online that will explain FTM in detail, and will also mention seeking advice from a medical professional...
Good Luck