Thanks for the reply. Perhaps I am confused.....
Looking at the control compartment at the top of the oven (and the fan located there), I see three wires coming off of the fan. One goes directly to the control panel board and the other two go to the door lock mechanism. The other wires from the door lock mechanism go back to the control panel.
The lower oven, which has the same fan shut-off problem, does not have a door switch or lock.
According to the service information pamphlet that was found inside the control compartment, the cooling fans are controlled via thermal switches found in the control compartment. However, the information states that they are in front of the fan on the floor of the compartment. Instead, what I have is one switch in front of the fan and one behind the fan (behind the fan housing). See page 3 of the PDF at the following link.
Here's a link to the pamphlet in PDF form: http://db.tt/PRPp8ygo
Looking at the diagram on the front of the pamphlet (which is duplicated on page 5 of that file), the switches I tested are connected via orange and blue wires (for the upper oven) and red/white wires for the lower oven.
For the upper oven, the other switch according to the diagram that is labelled 'high limit switch' is only operational when the bake or broil element is on; I believe this switch is located on the back of the oven.
Does it make sense that if the switches remained closed (even at a high temperature) that the fan would shut off before the oven has cooled off? My testing indicates that the switches are remaining closed (hence I can read a resistance across them at both room temperature and a high temperature after the oven has been shut off and the control panel has gotten hot from heat escaping up and out of the oven).
If it was not for the odd installation of the thermal switch (connected via blue wiring) behind the fan housing, I probably would have already just ordered new switches and given them a try. Perhaps I am a little too concerned about the one switch not being located in front of the fan as indicated in the PDF I linked to and (according to my reading of) the parts diagram you linked to.
Any insight would be helpful. Up to this point the contact I have spoken to at GE, who sent me the retrofit control panel kit, has told me they are not a service technician and cannot tell me left from right (fwiw, I did not expect them to be able to tell me much). Unfortunately the oven is out of warranty and they wanted to charge me to have someone come out and look at it.