I would like to help, but from your description, I can only make the same speculations you and your wife's provider have already made. The main possibilities are herpes, yeast, and trauma from frequent and/or vigorous sex. Herpes certainly can be transmitted when an infected person is asymptomatic; in fact, that's the usual case. (People with painful genital or oral sores tend not to have sex, so that those with asymptomatic infection in general are the most efficient transmitters.) But yes, herpes sores generally clear up within 10-14 days without treatment and a week or less on Famvir or other antiherpetic drugs--so that aspect argues against herpes. So it could go either way; you're just going to have to await the test results.
People infected with a particular HSV type, such as HSV-1 (the probable cause, if your oral herpes is the source of the present problem), do not get new infections with the same type. Even if you transmitted genital herpes to your wife from your oral infection, you are not at risk of genital infection yourself. Also, if this indeed turns out to be herpes due to HSV-1, the odds are your wife won't have any big problem with it. Most people with genital HSV-1 infection have few or no recurrent outbreaks--quite different than the case with HSV-2.
Don't let this bum you out. When all is said and done, even if it is herpes, it shouldn't have any significant long term effect on your wife's health and will have no effect on an unlimited and rewarding sexuality. All will be well.
I hope this helps. Best wishes-- HHH, MD
Thanks.