Balance the carbs. Probably the most overlooked thing to do.
And of course you replaced the crank seals right???
Also, clean out the clutch, new belt, make sure the rear suspension moves right, check for cracks in the suspension brackets, check ski wear bars, maybe replace them with carbides, Had enough yet??
Plenty of things to verify on a newly acquired sled. "best setup" depends on what type of riding you are planning on, and where you are located.
Of course your sled will always run better after you post some pictures of it on here...
P.S. Welcome to the club!!