Fan clutch

Can you post the exact code you are getting with a scan please.

What do you have for a code AND what do you mean "works".
There should be a ground (black wire) 12 volt feed from the fan relay (White wire) on the clutch power side. The other 3 wires are for the fan sensor. Solid gray wire should have 5 volts with the key on. Gray wire with white is a ground inside the ECM and the Dark Blue wire is a signal feed to the PCM.
With the key on and a cold engine the only wires that will show anything are the grounds and the 5 volt feed.

Have you checked the fan fuses and the relay?

OK that is a failure on the sensor side of the system. Check for 5 volts on the Solid gray wire, and a ground on the Gray/white wire.
What do you have for test gear?

OK test the wires above for powers and grounds. Should have battery voltage on White, 5 volts on the Gray wire and connection to ground on the Gray/White and Black.
There are a few connections in the lines so it's possible one or more have corrosion.
Testing them should show what's going on.

It could be but I doubt it. I think you will probably need to get an Oscilloscope to check if the signal from the clutch is actually getting up to the PCM.

Does the fan seem to work OK and you just get the error or is it locked on high?
You installed the new one, cleared the code and it came right back correct?

There is a TSB on these where the wiring harness chafes on the bracket and causes them to lock and throw a code. This isn't the issue as the cable would have come with the new clutch.

There is also a TSB that reprograms the fan operation but it doesn't apply to yours.

So either there is a bad connection in the signal wires to the PCM (doesn't take much) or the PCM itself is messed up.

It might be time to take it to a dealer or good shop and have them verify where the issue is with an OEM level scan tool.

Just to check do you have an autozone/advance/oreily around? Or similar place that will scan/clear codes free? Maybe have them scan it and see what code they get, then clear it. Some codes can be really stubborn and won't clear by disconnecting the battery. I always use a scan tool to clear them so I'm not sure if this one is a persistent one or not. Your description sounds like it is working OK, so you could try that. You could be chasing a ghost code.

Has to be a signal issue then. A VOM won't read the signal as it's a digital pulse not a sine wave or fixed voltage. Have you tried a continuity test from the connector back to the PCM? The dark blue and gray w/white would be the two to check.
Beyond that you need a scope or factory scan tool to read the fans duty cycle.
It's possible the old fans failure sent a power surge up the line to the PCM and the input is cooked but no way to tell that without seeing what the PCM is actually seeing from the fan.

A good shop with a good scan tool could handle it and be less $$$ the trick is finding the good shop.

Wish I could give you a better answer but without being able to see inside the PCM we have hit a wall. Where are you located state nearest large city, maybe one of us knows a shop in the area.

Please let us know what you find. I'm interested to see what it is.

Cheers, Ken

Albany, I'm 50 miles west of there. Used to own a shop on Central. Sold it and the new owners tore it down.
There used to be a good shop on Consaul Road and another was Capitaland over on Kraft, not the place on the corner of Kraft&Central but down on the left.