Your issue seems to follow a common thread. I have chased this issue on a 1997 Ford Thunderbird with the 4.6 liter V8 engine. The issue was the PCM had issues booting up. Until it boots, you will get the fan running on a low speed, because the PCM sends a signal to the CCRM (constant control relay module) to turn the fan OFF. This is a failsafe mode to be sure that the fan will run and provide cooling. Check the other basics before changing the PCM. See the other post regarding the 1997 Thunderbird that would not start, yet it would crank.
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