Wisdom teeth as explained to me by my "TMJD Dentist" can cause a whole wack of problems. I am not sure if it can cause TMJD related symtoms, but I am sure there are many nerve endings around that area.
Your body is made up of all these nerves that can run from head to toe, with your brain being a "Fuse Panel". A problem around one of these nerves can cause a problem anywhere along the way.. it's quite amazing actually.
My dentist told me that Wisdom Teeth should never come out, UNLESS they are causing problems. Some people's jaw has shifted because they had their wisodm teeth taken out, and in turn developed TMJD or worsened their condition.
In my case, I am getting all 4 taken out as one if servely impacted (ironically, on the side of my ear problems) and the rest are impacted as well...
The search for a diagnosis is long and painful...