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Do you have access to a scan tool that can read the Pids?Is this an automatic system (buttons ) or manual (knobs)?
Okay see the testing steps in the link below for checking the clutch operation and I have also enclosed the wiring diagram for the system for testing reference. Have a look and see if these steps will help you get this resolved.https://dl.dropboxusercontent.com/u/104923897/AC%20clutch%20Sept%209.pdfhttps://dl.dropboxusercontent.com/u/104923897/Clutch%20wiring%201%20Sept%209.pdfhttps://dl.dropboxusercontent.com/u/104923897/Clutc%20wiring%20Sept%209.pdf
The ground is supplied to the relay from the PCM and if the TP sensor is not stuck in the WOT mode then that usually means the PCM is at fault. Are you getting any fault codes?
Have a look at your TP voltage to be sure its reading closed throttle and that the voltage comes up when you open the throttle as well.
The TP looks normal . Okay then you loosing your ground from the PCM, I would suspect the new PCM is defective especially if the system cools properly with the relay grounded.
There are known issues with the windshield leaking on the 2002 F 150s where water leaked in and dripped on the interior fuse panel and the GEM module which mounts to the top of it, is the voltage steady on the interior fuse panel as well?
What is the voltage reading at the battery, is it pulsing as well?
Dose not make since if it pulsing at the fuse panels. Battery voltage at the fuse panels should read the same as the battery voltage at the battery.