Welcome to the STD forum. I'll try to help. Responding initially to the plea in the title of your question, I believe I can indeed offer "peace of mind". I doubt you or your partner has a current HPV problem.
It would be interesting to know the evidence that your partner still has HPV after 3 years, apparently long after her warts cleared up. The large majority of HPV infections resolve, and the "low risk" HPV types that cause warts ("low risk" means not strongly associated with cancer) typically clear up within 6-12 months. Therefore, it seems unlikely your partner still has that HPV infection.
For these reasons, I see no reason for you to have avoided genital intercourse with your former partner. In the off chance she is infected, all that would have happened is that you will catch it too. But that's going to happen someday anyway, and if you have otherwise been sexually active you can assume you already have had at least one HPV infection. Everybody gets it within their first few lifetime sex partners. Fortunately, the large majority of infections never cause symptoms and go away. Even if you get penile warts, that should be viewed as a trivial health problem -- an unpleasant inconvenience, but that's all. Most genital warts are easily treated and in any case go away even without treatment, as I said above.
In any case, if your partner had an active HPV infection when you were together, you were at little or no risk through hand-genital contact or oral sex, and there was no need to "keep your hand away from your genitals" or to use antibacterial soap. I hope your compulsion about these things, and avoiding vaginal sex, was not an important reason that you and she broke up. That would be unfortunate, as it was unnecessary. But I can imagine that such behavior could be pretty stressful in any sexual relationship.
As for sex with a new partner at this time, there is nothing you need to discuss with her about your previous partner's apparent past HPV infection. If everybody who had sex with an HPV infected person knew it and told future partners, then nobody would ever have sex without discussing HPV. You need to look at catching genital HPV as a normal and expected event. Not desirable, but normal. Also, in the not too distant future, Gardasil -- the HPV vaccine that protects against the 4 HPV strains that cause most warts and cancer -- will be approved for use in men. You could be immunized to prevent future infection with those very common HPV types.
Finally, HPV doesn't cause pimples -- and the inner thigh is a common site for garden variety pimples. That problem has nothing to do with HPV. For all these reasons, I agree with your doctor.
So there are the "solid answers" you seek. In addition, you can look at any of several reliable websites for additional information. Try www.cdc.gov/std, www.ashastd.org, and www.westoverheights.com. Bottom line, as I said above: You have no obvious HPV worries here. All is well.
I hope this helps. Best wishes-- HHH, MD