Ford's recommended fix for third-gear shudder (around 40mph, I'm guessing) is to change the filter and fluid, using 100% Mercon fluid. After replacing the filter, flush out all fluid, including in the torque converter, by disconnecting the fluid line at the radiator (the one that brings fluid out of the transmission) and run the car in park until it's dry. Pour through a quart to clean it, then reconnect and fill.
I have also managed to correct the problem by staying out of the 39-43mph range, and using a lead footed approach approaching that shift point.
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