I have an idea for a possible fix for the extruder. The upper extruder is almost entirely enclosed, I think that the fan which blows air on the hot end fins is only creating a recirculating air pocket. Kind of like what happens in the bed of a pickup truck with the tailgate up. Inevitably, this pocket will heat.

My idea is to add a couple vent holes in the upper extruder casing. This should make it behave like a venturi, and suck cool air in from above. Since I don't own a fifth gen Makerbot, I haven't had a chance to test the idea, though.