Henry,
Don't know if you found your problem but I know with my 98 500 sportsman that I had, the wiring had issues of being strung very tightly. I put more loom on and rerouted alot of wires on that bike to prevent chafing and unnecessary grounding. I did have a wire break in the harness just as it enters through the engine casing going to the stator. It took me some time to find this but the bike would still start. Perhaps it was a nonessential wire but it did affect the charging of the bike as the fan would not run and the lights would pulse as the bike idled. Trying to find the problem I disconnected many components only to find the bike would still start. The main wire from the frame to the top of the engine was another issue. I replaced two of those. A multimeter is a must for troubleshooting the wiring. I know my new 2008 won't be as user friendly when it comes to troubleshooting problems. Also I know of about 3-4 guys that had problems with worn out cams. It seemed to be Polaris had alot of problems with these cams. I personally didn't have any cam issues with my bike but my bike didn't have high mileage. Hope you have luck with your bike .