Losing my mind with electrical issues.

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You got wires that dump the cruise on the brake pedal and clutch
Check those harnesses real close and the switches for obvious problems
A good scan tool can see when either of those pedals are depressed? Maybe?
I think my NGS would scratch it
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You got one or two grounds above the drivers feet
You got one or two in behind the left kick panel
A Ford EVTM for your car would be a good investment (shows every ground location and has pics)(all the schematics) etc.
I only have one mustang evtm a 1989 I think or I would post pics for you
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Cables seem to be fine, cleaned a large majority of the grounds as well. Replaced both cable ends as well. Its something piddly.

Cables?? The 2002 uses an electronic speedometer with OSS that is run through the PCM. I tried something yesterday on my '02 but didn't do what I thought. Was thinking the fob battery was your issue so I took mine out hoping it would replicate your issue, but it didn't. Still trying to wrap my brain around this.