This is just my 2 cents!
My 93' toy pickup 22r ticked, my 99' tacoma 3.4L ticked, and my 97' 4runner 3.4L ticked, haven't yet heard ticking from my 06' 4runner 4.0L.
But I haven't been driving around the with the window down yet to hear it. Seem pretty strange you wife hears it and you don't.
Here is a story from my 99' tacoma, after my 60k service at the dealer I was noticing a louder then normal ticking so I brought it into dealer and they said thats normal. About 200 miles later i was driving over the mountains and truck freaks out starts shuttering. Find out one spark plug shot out the engine because the dealer had stripped it in the engine block. THIS IS WHY I DON'T TRUST MECHANICS!
I will be interested in finding out what it is.