How to align front and rear sprockets:
the whole notch on the axel adjuster and swingarm is not a 100% exact & 100% precise system. everything is not built to those exact tolerances.
this tool should be in every home mechanics box.
remove your chain guard.
you attach it on the rear sprocket and point the arm down the chain to the front. after you've established the proper chain slack (by adjusting both left and right side to the same adjustment notch). you then mark the left/drive side notch with a black marker. this is your fixed side as this this adjustment is critical for proper chain slack.
then with your tool in place and looking down it and the chain towards the front sprocket, you adjust the right/disc side notch so the arm of the tool and the chain are as parallel as possible. sometimes this is the same notch as the left sometimes is 1 or even 2 + or - of the left side. doesn't matter as long as the tool arm and chain are parallel.
when you've found the proper right side notch hand snug the axle bolt (you did upgrade to the updated Fuji nut style from PC right? vrs the old crap style castle nut). then torque to 72ftlbs and mark the right notch with a permanent marker too.
now your sprockets are aligned to each other and your chain lasts longer. by marking both notches you can quickly get back to this adjustment if you need to change a tire. over time your chain will stretch and so move each notch up 1 respectively to tighten your chain.