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I just rebuilt 96 Polaris xcr600sp and am thinking the coolant is not circulating.

Is there a thermostat?

The bottom hose from water pump is cool while engine hot and upper hose running to above cyl is hot.

I've only ran it sitting still so far.

I bled the line by opening bleed screw above cylinders on the pipe running accross top cyl
 

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Some have t stat mine doesn't call a dealer and ask if it is listed in the parts book for your sled . It sounds like you have an air lock.
 

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If you have the update, the t-stat will be in the hose between the top water rail and the brake caliper,you can't miss it its an aluminum housing about the size of a tennis ball, there is a bleeder on this also. Try putting a piece of 4x4 under the ski on the recoil side to make sure that the coolant bottle is the highest point of the cooling system ,this helps bleed it, this is how I do mine I have a 97 XCR600 se.
 
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