Sounds like main cpu fuse or one of the sensors
First get the service manual so you have test proceedures and diagrams to locate the sensors such as oil and overheat and the main cpu fuse. Polaris had a limp in mode on their machines when the cpu lost primary power or it did not get a reading from one of the sensors. When it goes into limp in mode you will have smooth operation through a certain range of the throttle then at greater throttle the rpms will not increase and the engine will run rough. The main fuse is the most likely since if it lost primary power while running it would stall. On restart you would be starting in Limp in.
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