It still (to me) looks like you just need to true up the tire by either tightening or looseninf the adjustment screws. My rear looked similar when I had it apart changing to spoked rims and then back together. All I did was eyeball it on the jack stand and then tighten her down. Of course the adjustment lines didnt match up, but the rear is as true as its gonna get. Other than that, I dont know what to say. Can you take a pic similar to what you recently took, but I would like to see the whole tire in the swing arm without the fender on. Good luck, bro!
Jeff

Best looking black girl around! 2004 SM-spokes, solo seat, lowered rear, 14 in apes, bobber rear fender, no front fender. Flat black all the way around. Jeff