The motor will fit the chassis but the electrical system is completely different. 2000 is when they upgraded the headlight and changed the handwarmers so they used a different harness and stator. The stators are the same for 98 and 99 and won't fit the 2000 and up engines. You would have to put the 98 Harness, warmers and headlight on the 2000.
Sorry I was wrong, it looks like the 99 is a twin also. According to the Microfiche Diagrams on Ronnies.com they were twins in 98 & 99.
Not trying to argue with you rp7x since you're looking at it but if yours is a '98 600 with a triple it makes me wonder if someone changed the motor already? Anyway good luck with the swap, hope it all works out for you. These are great sleds!!