Hi 68 S code, Kinda a late comer to this post/thread, but I thought I'd add my 2 cents.....
If the engine won't fire on starting fluid, That's a STRONG indication that it's a spark related issue, not a fuel/heat issue. The first thing I'd change is the coil, especially if your running a repro yellow top coil, as they really suck, especially when heat soaked.
If a new Motorcraft coil doesn't help, I'd temporarily add a decent mechanical temp gauge, and know for sure what the coolant temps are running.
Lastly, If your running the dual diaphragm setup and are having idle speed (advance) issues, try another ORIGINAL thermostatic vacuum switch, as the repros suck for this part as well. You should be able to troubleshoot the advance system by initially hooking the port on the metering block directly to the outer advance port, and leave the inner advance port open. That should bypass the whole dual system, so you won't get the increase in idle speed at high coolant temps, but the car should behave normally otherwise once you reset the timing
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Let us know how you make out....
John
BTW, I'd be surprised if your car came with a dual diaphragm setup with a C6, as that could be kinda a safety issue.... The dual diaphragm system/thermos switch setup was designed to increase the idle speed once the coolant temp got too high to aid in cooling. A sudden increase in idle speed on an automatic car could cause the car to lurch forward unexpectedly, another thing that could suck ....