My wife is 39.

I received oral sex from somebody els who we can confidently assume has been exposed to or has STIs.

I have completed the full STI panel at the appropriate exposure windows, they all came back negative.

I'm aware that there's no reliable way to test for HPV in males.

My wife is the only person I've had sex with otherwise, and I'm the only person she has had sex with ever.

Question:

With HPV being the remaining concern, we're wondering how to proceed in having sex again in the safest way possible. We were considering getting the HPV vaccine for her. There's concern about the efficacy and safety of the HPV vaccine at my wife's age. We're not sure of the risk of transmission of HPV given the act above, as well as if my body may have fought it off after the 2 or so years, as I believe I've read can / does happen. We also understand that with regular pap smears / check ups, risk of HPV resulting in cancer is low, and if caught early can be treated relatively easily. I'm also curious about rates of HPV leading to cancer when the exposure happens at her age (39).

So as a single question, what would your advice be for the safest way for my wife and I to have sex again?

1.  Although your casual partner may have been at risk for STIs, oral HPV infections are far less common than genital HPV infections.

2.  A single act of receiving oral sex does not result in transmission of HPV, if present in the oral cavity, in the majority of exposures.  

3.  Had you become infected with HPV, after two years, the infection would likely have been eliminated by your own immune system

Giving these facts, the likelihood that you have active, transmissible HPV is low.  If you remain concerned about what is typically an innocuous, readily managed infection if present, for your wife to get vaccinated would reduce the very small risk of infection to virtually zero.  There is no reason that vaccination at her age would not provide protection after receipt of two doses of vaccine.  

There are no data on age-related HPV progression rates but there is no reason to worry that they are higher for her than others

Thus my sense is that there is very, very little risk for her to acquire HPV if you resume unprotected sex at this time.  In the tiny chance that she did become infection the composite risk of infection progressing to cancer, particularly if she does get regular reproductive health checks, is virtually zero.

I hope that this perspective is helpful.  EWH