It's actually really hard to not have your wheels aligned naturally, unless you did not undo one side of the clamps before adjusting the chain. But this is a very detailed and clear commentary of the adjustment process, thank you for posting.
Your video covers alignment from front to back but when I install my rear wheel, the right hand axle sleeve seems to be too far inward on the swing arm. Any tips on this alignment? Ie..do both sides sit flush with the edges of the swimgarm?
If I am understanding you correctly, yes, they sit flush with the swingarm. I don't see any other details in the service manual for any other type of alignment either to help diagnose the problem. Are you saying your wheel seems to be misaligned left/right (off-center) from the center of the bike?