I had same problem with 2001 550 sportsman, alignment good, belt good, dealer replaced what he called grooved primary clutch...$400! Problem came back within 100 miles of riding!
Son and I decided to look into it ourselves, tested with clutch cover off, close observation looking and listening, we determined that the engine braking portion of the primary clutch was not releasing as it should, putting a load on the gear box, making it very difficult to shift, and causing the bike to creep at idle rpms.
Cheap fix...We simply changed from the engine braking system model drive belt (which is slightly smaller in diameter than standard) to a standard sized belt (for machines without engine braking clutch installed). The standard sized belt rides just a tad higher in the primary clutch, and does not engage the engine braking portion of same, and does not ride in the "groove" the dealer described.
The creeping and shifting difficulty was gone! Have ridden in this configuration for several hundred miles since with no difficulties. And....there still is noticable engine braking available, though not as much as before.
Go figure. May not be your issue, but worth considering.