What's MOST important IMHO is making sure sprockets and chain are aligned with each other.
I put bike on center stand, crouch down behind bike with transmission in neutral, and spin spin spin the rear tire while looking down the length of the chain between the two sprockets.
If chain is not freely flowing in a straight and unimpeded manner I know something is not correct with my axle alignment.
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2008 WR250X
Gearing: 13t - 48t
Power Commander 5 / PC-V
Airbox Door Removed - Flapper glued - AIS removed
FmF Q4
Bridgestone Battlax BT-003rs