Hallo Adam, and welcome! Let's take a look at your inquiries:
1. It is possible that your partner has passed to your her particular strain of HPV. Then again, she might not have....I keep posting this: HPV is annoying and really damn frustrating because no one knows when you've stopped being infective. Because she's been normal recently, that probably means that the virus isn't active and she may not have given it to you. Even if she did, the kind of HPV that shows up on pap smears is the oncogenic type/cancer causing type that causes CERVICAL cancer. As you have an output and not an input, you're ok on this
RARELY, it may cause penile cancer, but this is reaaallly uncommon.
2. As said in #1: you may have it because you two have been together for a while. For example, I think my current boyfriend is my HPV source and I think he contracted it YEARS ago (he's 31 now and was sexually active at 16, and NEVER SHOWED ANY SYMPTOMS) and I was only with him for about 7-8 months before I showed signs....admittedly I think it was because I got pregnant (this is an immunosuppressive time for women) but yeah. They don't test for HPV in men, though, and it seems like she doesn't have the wart causing kind so you may not know for sure.
3. From #1 and 2: I think your partner has a cancer causing HPV type, which for men doesn't usually cause any problems. This is why vaccination and treatment usually has centered on women so much as it is a potential cancer burden that they face. HOWEVER, in another year or so, they may begin vaccinating young boys as well (thank goodness). So your main concern is passing it to another female should you have another partner in the future.
4. HPV ano-genital strains are generally picky; they don't like anything except the ano-genital mucosa. It CAN possibly be transmitted to the head-neck region (mainly thinking oral mucosa) but it's pretty rare. I think you guys are safe as far as sexual practices go---I would just say that, on chance that you are now carrying HPV, to use condoms during the times that your partner has abnormal cell changes going on, so that if you are carrying it she has less exposure to the virus.
5. It's hard to say how your partner will be in the future; since she's been good for the last 2 years that's good news---just make sure she keeps going to see her gyn every year, though. Once you have any kind of HPV I think it's advisable to go yearly to make sure you're absolutely on top of your personal health care.
Best wishes and health to you; keep us updated!