Alright, so this sounds EXACTLY like what is going on with my 4Runner.
Its not the fan clutch... The problem is most likely a blocked heater core. I know this is the worst news but at least the engine didn't overheat! I, just like you, are fairly attentive to various operations of my car. I caught the same thing start happening on my last road trip. I started to have to downshift manually and rev the engine whenever I stopped for a prolonged period of time. This was the only reason I could keep the temperature down.
Do this test: allow the car to begin to overheat, when it first begins overheating apply the throttle in park (or neutral) and rev the engine to 1500-2000 RPM and hold it there. There may be a momentary jump in temperature in the first few seconds, but it should begin to cool.
Also: while stopped and engine warmed up to operating temp, turn on the heat on full blast. Typically a heater core will result in loss of heat while the car is not moving. You could miss this symptom because most of us have no need for heat in the summer.
To test thermostat: (and my guess is that the thermostat is not your issue) allow the car to warm up, touch the upper and then lower radiator tubes (carefully they will be very hot, or infrared gun them) they should both be warm/hot. If one is seriously off in temp, then it can be the thermo.
Hope this helps. Unfortunately the entire dash needs to be removed to replace the heater core. Its costly as far as labor goes. May as well do the evaporator core at that mileage so an a/c recharge would be in order. Best of luck! My money is on the heater core... Most mechanics, unless they really know cars, will go on a wild chase replacing the coolant, radiator, thermostat, fan clutch, water pump etc before they finally track the ACTUAL problem down