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Does it have the OEM Ford MotorCraft ignition control module? Here's a link to an extensive DIY testing approach, but for $30 I'd probably buy a generic replacement and see if it doesn't fix the issue. Sounds to me like your module is getting heat soaked on the long run with higher under hood temps, and starting to break down and give flaky signals.
Link - Part 1 -How to Test the Ford Ignition Control Module (Fender Mounted)