You said you were offered the old parts.
I assume this population includes the old fan motor.
Does the old fan motor spin when you apply 12 VDC to its terminals? If so, you did not need a $ 400 replacement at all.
If you Google "KLR650 wiring diagram," you'll see the fan relay terminal is connected to the FAN SWITCH (a thermal switch that closes at a coolant temperature areound 200 degrees F., called by others a "sensor," or "relay," but to me is a thermal switch).
Now, discussion becomes complicated. The TEMPERATURE SENDER in the cylinder head controls the position of the TEMPERATURE NEEDLE on your TEMPERATURE GAUGE; NOT the fan switch (called by some the "sensor," or "relay") at the bottom right of your radiator.
An AIR POCKET in your radiator may prevent adequate coolant circulation at idle, causing the TEMPERATURE SENDER in the cylinder head to register a high temperature, while the coolant in the bottom of your radiator had not reached sufficently high temperature to close the FAN SWITCH, activating the FAN RELAY, and turning on your FAN.
The cure for an air pocket in the cooing system is BURPING; one burps the cooling system by operating the engine with the radiator cap OFF 'til the coolant temperature rises sufficiently high so that the THERMOSTAT opens, circulating the coolant. An air bubble will exit the open radiator neck at that time, the RADIATOR CAP can be reinstalled, and the COOLANT RESERVOIR filled to the proper level.
The above paragraph describes the burping procedure, eliminating air pockets that may result in a high temperature gauge reading (from the TEMPERATURE SENDER in the cyclinder head as mentioned) without sufficient coolant temperature to close the FAN SWITCH at the bottom right of your radiator (again, some refer to the thermal fan switch as a "sensor," or "relay"), activating the fan realy and in turn the fan motor.
I've tried to explain, the TEMPERATURE GAUGE and the COOLING FAN actuation circuits are SEPARATE; the FAN SWITCH doesn't know or care what your TEMPERATURE GAUGE says; the fan switch, simple thermal switch that it is, only knows whether the coolant surrounding itself is high enough for it to close, providing a GROUND to the FAN RELAY and actuating the fan . . .
Your mechanic should know these basic functions, how to configure and to test and verify your motorcycle's roadworthiness.
I think you need an ethical, knowledgeable person (professional mechanic or neo-competent gear-head) to examine your bike, and, favoring your best interests, advise you.
I suspect your cooling fan's o.k.; that any problem is the result of electrical malfunction (e.g., fan fuse, fan switch, fan relay or associated wiring), or perhaps of air pockets in the coolant.
I further suspect the mechanic seeks to rip you off on chain and sprockets; suggesting you'll trash your crank bearings as a consequence of worn chain-and-sprockets appears false and irresponsible to me.
While the Service Manuals provide service limits for many components (I'd hope you have a copy of KLR600 and KLR650 Kawasaki service manuals, or a Clymer), you're on a steeply-sloped learning curve regarding maintenance of your KLR650.
I have serious doubts regarding the competence and ethics of the mechanic and shop with whom you're dealing.
Your descriptions of your interaction with the dealership appear specific enough; I think you can name the dealership without fear of libel or defamation litigation.
Reviewing, for your fan to work, the fan motor must be sound (TomatoCity tells you how to test that; ground the lead to the FAN SWITCH and see if the fan spins; test will work withether ignition switch is ON or OFF). For the fan to cool the engine properly, the FAN SWITCH (yeah, they call it the "sensor," or "relay") must CLOSE at around 200 degrees F.; the Service Manual tells how to test this, if necessary. The FAN FUSE must have continutity (easily tested with a multimeter). And, the FAN RELAY must close its contacts, when its control terminal receives a GROUND from the FAN SWITCH (yeah, the famous little gizmo mounted in the lower right of your radiator). Finally, the coolant system must be free of air pockets (the BURPING procedure mentioned above) for the cooling system to operate properly; burping affects operation most critically at idle; at higher rpm, sufficient circulation may be possible, even with air pockets present.
My overall suggestion: Cut your losses, find competent help and advice.
CAVEAT: The functions and procedures mentioned in this post reflect my own perceptions and opinions; corrections and clarifications welcomed!
Just thought of something that might help explain the distinct separateness from the temperature gauge and the fan switch:
The TEMPERATURE GAUGE receives an electrical signal from the TEMPERATURE SENDER in the cylinder head; the signal is proportional to the CYLINDER HEAD TEMPERATURE, without regard to coolant . . . the cylinder head temperature will register, even if no coolant whatsoever is in the radiator.
The FAN SWITCH is open, no contact, unless the coolant surrounding it approaches 200 degrees F.; at that point, the switch CLOSES and reflects a low-resistance contact with chassis ground. If, for example, there is no coolant in the radiator, the temperature gauge may be well into the red zone; however, without the coolant to transfer sufficiently high temperature to the fan switch to cause the switch to close, the fan switch will remain open and the fan will not operate (despite extremely high cylinder head temperature).
THIS IS AN EXAMPLE ONLY; DO NOT operate your engine without coolant!
My point: The temperature sender and temperature gauge, when isolated, work independently of the fan switch/fan relay/fan fuse/fan motor. With proper coolant quantity and circulation, a relationship can be inferred, but--no direct relationship exists between the two circuits, when analyzed separately.
TEMPERATURE SENDER in cylinder head: Wire goes to TEMPERATURE GAUGE.
FAN SWITCH in lower right of radiator: Wire goes to FAN RELAY.
Last edited by Damocles; 05-12-2011 at 08:09 AM.