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1994 gs klze, auto to manual swap, car had an engine harness fire, replaced the harness with a new on from mazda, now the cooling fans will not work at all. All the circuits have power, seems as though the ecu is not switching them on. I can ground the relays and they will both come on full speed. Any help would be appreciated.

Is the coolant temp sensor plugged in?

Yes, both of them.

well good job on the replacement , so when the engine gauge gets to the operating temp few moments after the front left fan ( facing forward engine) should turn on . if not under the fuse box check fuse for cooling fans make sure its not blown , also check the connector under the fuse box its a small white 3 or 2 plug connector if thats not hooked up or lose the fans wont turn on . if thats all ok facing the engine forward top left corner passanger side there is 4 relays , one of them is the fans cant remeber which one it is but look at the online manuals and it will tell you which one . if thats all ok make sure the fan ,motor didnt burn up remove conector and add direct power and ground to fan ans should turn on . im sure you have a small issue making the fans not turn on . any questions let me know

All fuses are good, it is a problem around the relays, I believe.

Yea man check relays and switch them around they all the same anyways if you turn your ac on the other fan will come one right away so remove the relay until the fan for ac turns off then you know its a know good working relay and switch it with the engine relay fan and should pin point your issue .

Check relays according to FSM, as well as coolant temp sensors.
Why is cooling fan supposed to work? Is your engine overheating or do you think that cooling fan should work when engine is on?
On my aunts camry BOTH fans would constantly run, I checked all the fuses, relays, etc and finally found a problem-whomever owned it before didn't have a coolant sensor plugged into the radiator. Went to junkyard and got one from parts car and now car runs quiet.

Fans will not even come on while the a/c is on. I think I have found the problem. Purchasing a new harness and fuse box from another member, hopefully everything will be okay now.

Sounds good let us know how it goes

Been digging further into this again. Found a few bad relays under the coolant over flow bottle, replaced them but still no fans.

It seems as though the ecu is not outputting the signal to turn the fans on or it is not receiving coolant temp data.

I have found this connector that is not connected to anything?

I can bridge the wire and trigger the low speed fans. What is it supposed to be plugged into?

I am almost thinking I have a power problem since my speedometer doesn't work either. All fuses are good. I just don't know what else to check.