You mainly want to make certain that you don't set the chain tension too tight. (The most likely cause of output shaft/sprocket problems)
Many riders coming from street bikes get worried over the apparent "slack" in the AT chains when the bike is at rest. Remember that you have almost twice the rear suspension travel and the rear wheel moves in an arc. The chain will be at it's tightest point when the countershaft sprocket, swingarm pivot and rear axle are all in a straight line. Once the rear wheel passes this point the chain will start to slacken again. At rest the AT chain should look more like a MX bike.
Best way to set tension is to put the bike on a good stand, remove one suspension link (to remove the damper and spring from the system so the swingarm can move freely) and prop the swingarm up so all three points mentioned above are in line. Pull the chain back until moving the rear wheel causes a bind....then move the wheel forward until spinning the rear wheel is smooth. Set the tension there, reinstall the suspension link and put the bike back on the ground. Measure this amount of chain slack and use that as your basis for setting the chain as it beds in and wears a bit.
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