SfloriII
I'm 100% certain that your records (you do still have them don't you) state that the engine wiring harness had been changed by the dealer under warrenty. Not sure of any of the other wiring harnesses though. Off the top of my head I can't think of any relay located underneath the passenger side dash that could be ticking and causing your issues. I would suggest looking for the wiring schematic in the CD and see what all is tied into the cruise control circuit and start from there.

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Jim