This actually sounds a little like HPV to me, but more like Herpes.
Herpes can be mysterious with no discernable pattern of onset. It's rarely obvious which is why so many of us post here. heh.
Obviously, the best thing to do is get tested some more.
Unfortunately, men cannot be tested for HPV but your wife can.
So, you = HSV blood test and(if possible) have a swab taken from one of your outbreaks.
Wife = same as above but also get HPV test.
That should clear everything up (unfortunately, not a pun) :-0
Sorry to hear about this, but one positive is that you guys are already together and all. Catching an STD and being single is a whole different world which can be pretty depressing and lonely for some.