Courtney,
You are correct to say that the issue with AWSMDS wasn't one of aircraft fatigue although it was to do with the fatigue or failure or the followup system. AWS was not designed to be manually over-riden. The systems engineers at Warton had no concept that a pilot would wish to move the wings manually. Also, there was a belief that a pilot would never use an intermediate wing aweep setting since they were not cleared for service. The system failed to come into service in the RAF due to a lack of knowledge at middle management. As mentioned, the RSAF operated the system throughout the life of the aircraft without problem.
The story of the aircraft fatigue is a different one. The fatigue was recorded at the different wing settings and at certain G. The factoring to ascertain the total aircraft fatigue was based on the profiles in the Statement Of Operating Intent. Engineers believed that these profiles were accurate and aircrew could not be bothered with it. At the end it was very simplistic and was like trying to crack a walnut with a sledge hammer.