First, let me state that I believe the enemy of reliability of virtually every automobile (many components) is heat and this is also true of many boat components - especially the drive trains.
There are many heat sources in the Ford GTs - and a number of them can be dealt with easily. I would say that the worst case combination, under the worst case conditions of external temperature and driving methods (track racing or mountain road scurrying) could create temperature problems in many areas of this wonderful car.
The first modifications to my vehicle (4 months after purchase - when the snow melted) were to install the Rear Exit Headers (M-9430-GTX) and the Transaxle Cooler (M-7095-GT) from Ford Racing, knowing that I wanted to track the car on various occasions. This did the following:
1) Elimination of the Catalytic Converters, which are a major heat generator, reduces the temperature under the clamshell.
2) Elimination of the factory muffler removes a heat generator, and also is a major improvement in letting increased air flow through the engine compartment, as the muffler systems block the air exiting areas with hot components. The exhaust pipes of the Rear Exit system stay low through the engine compartment prior to coming up to their exit locations.
3) The transaxle cooler lowers the gear oil temperature in the transaxle, which everyone has been talking about already. Furthermore, in conjunction with the removal of the heat source and flow blocking muffler, and radiation from the catalytic converters, my transaxle should be running cooler than most of the other cars with different components. The fact that the transaxle oiling system was designed to include this cooler (including the mountiing positions) shows that Ford originally intended to include it in the design (I believe the prototypes all had them), but removed it as a cost cutting measure in the final design.
I have never had a clutch problem in this configuration, including running on the track at Miller Motorspoorts Park in 109° F temperatures running in 2nd (mostly) and 3rd - reaching 4th only on the main straightaway. And, at one point the engine reached its temperature limit (242° F), cutting off cylinders for about ½ mile. Yet, the air flow through the engine compartment (the license plate is removed for track time) kept the other components as cool as was possible.
If you can find ways to eliminate, minimize or reduce heat under the clamshell, you will keep your gal running as reliably as possible.
PS - this is not to say that there is not another cause to the flat pedal phenomenon, especially after reading MR2Race's post in the other thread, however, I still believe that heat reduction will only make your GT experience much better.