90% of people will clear the HPV virus from their bodies within 2 years. Chances are excellent that you have, if you got it.
Yes, HPV can enter through the scrotum. It's a different virus than herpes, which can't. Warts can also appear on the scrotum.
It's been 2 years though - I think you can let it go now. You used condoms, which offer significant protection.