are there signs of leakage? a sure sign of a water pump going bad is to check the 'weep hole' located on the underside of the water pump...kinda hard to see and get to with the stock fans on and such. it wont always leak enough to tell either, but if you notice any coolant on your crank pulley or belts after turning the car off (wait a few min) that's probably the case.

the other thing is to make sure your fans are actually working. the clutch fan mechanism can go out but its more likely the secondary fan used for a/c and when the temp gets over a certain point, isnt working. you can tell if part of it is working if you turn the a/c on and hear it click on and you can see it if u put your head over the engine and look forward into the shroud.

or you might have air in the system. turn the hvac controls over to the heater hot side in the car and then run the car and top it off, you might have to let the car cool, open the bleeder valve and do it per FSM specs, which sucks.