Are you sure your water pump isn't failing? That would explain the codes, limp mode with lack of throttle response, and fan running at full speed. It could be the change to the harness and this issue are completely unrelated. My water pump went out without any warning at all. I had just completed a 900 mile road trip, and the following day it stopped working after driving about 10 miles from the house. There were no codes or signs of failure prior.
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