hard to say without experiencing your problem in person, This might sound weird but,, my 97 had a problem, it would intermittently die or bog, but would restart and run fine, it turned out to be the spark plugs were causing the problem, mine originally came with champion plugs(from the factory), but all the other sleds I had I always used NGK spark plugs, so when it came time to buy replacement plugs I bought NGK's and used them, it turns out thats when my problem started and by chance while I was on a trip and experiencing this problem and fouled out the plugs, I didnt have any spark plugs so I got some from a buddy(he had the oe champion plugs that my sled came with), after putting the champion plugs in, the sled ran great and even sounded different. I never had another problem again. I have only heard of two dealers that I have gone to that know about this problem, they told me that the NGK spark plugs, cause the ignition modules to go out of whack, they told me that if your polaris came with champion spark plugs use champion, if they came with NGK, use NGK.
like I said, I dont know if this is your problem or not, but it might help