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The ECU only uses one sensor to measure water temp, if it is displaying temperature properly then it should know when to activate the fans. Does the PFC have some sort of parameter in the software to tell you it is trying to activate the cooling fan?
It sounds like there could be one of three things wrong:
1.) Relay doesn't work properly.
2.) Relay is not wired properly to power, signal, or to the ECU (which will be GND when activated). You should be able to measure +12V on the wires I've outlined in solid colors, or 0V on the wires I've outlined in dashed colors.
3.) Something inside the ECU is damaged and it isn't able to ground the relay properly.
By the way, I'm not a PFC expert but I don't think you should see +5V on the G/B wire. It should be about 12V or 0V. If your car will run OK with the stock ECU, maybe you should try that and see if it activates the fan. If not, see if you can get ahold of a friend's PFC or try your PFC in another car to see if things work differently with that car's wiring and/or relays.
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