Overheating after running for about 10 mins fan not working and I have tested the connection it's getting fire to the fan

 

You can test the fan motor with 12 volts direct to see if it's ok. This year model had a problem on the pdm modules at the front of the machine as one of the things it controls is the fan.Item #11. Dirt Cheap Yamaha, Honda, Arctic Cat & Polaris OEM Parts & Accessories – Cycle Parts Warehouse

 

The fan working when I run straight current to it. But now as soon as I start it the hot sign is flashing on the odometer

 

Don't have the 06 efi manual,BUT have the 08 which does show the fan has a relay under the front panel powered by a circuit breaker on the harness leading to it that can short out and stop the fan from operating. Plus the later model efis had the temperature sensor on the left side of the cylinder that had a dual purpose and sent info to the brain box(ecu) on when to kick the fan on and also triggered the hot temperature indicator on the speedo. Can't remember on the 2006 model,but you can take an ohms reading on the sensor when cold and also when the engine is warm and resistance reading should drop. If it doesn't the sensor could be bad and needs to be replaced.Check this out and also under the front panel for the relay and circuit breaker.Best if you have the correct year model manual that I don't have that can help you track it down along with any future service/repairs. 2006 Polaris Sportsman 500 EFI Service Manual PDF Download

 

How can u tell if the water pump is not functioning properly

 

Open the radiator cap. When the thermostat is open coolant should should be visible flowing back to the radiator and circulating.

 

The coolant flow like it was suppose to but the hot light was still on u think it could be the ecu box and if so how can u tell

 

Down load the correct model manual for your machine I posted a link for! Shows all the trouble shooting steps along with a good wiring schematic. Better than just guessing or throwing unnecessary parts at it to find the problem. Well worth the 5 bucks..