I just installed a new rear wheel on my bike and adjusted the chain and made sure the chain adjusting bolts hit the same notch on the bolt. After doing that, I spun the tire on the centerstand and I'm hearing a slight knock (not the regular clicking noise) in the chain, as if the chain is not aligned. I also took a quick look at it with just my eye while staring at the back of the bike, and it looks as if the tire is not straight up-and-down. Almost as if the bottom of the tire sits further to the left than the top of the tire. This is the first new tire and it's only got 6000 miles, so I have no idea what it could be. Is it just my alignment that's off, or am I just tricking myself and it's actually fine? Is the chain supposed to make that noise??

 

No it should NOT be making that noise. Are all your spacers installed and on the correct side?

The chain should run straight from the front sprocket to the rear sprocket. There should not be a lean to either direction. Be sure that you use those notch's only as a guide...they are NOT exact. Also be sure that the chain has about 1' of slack. I wouldn't say any more then that as there's not a lot of torque running thru these 250's.

 

The manual calls for 1.4" -1.6" of slack in the chain, i run mine right at 1.5" of slack.
Anyway i would pull the rear wheel again and look to see if somehow the bearings or spacers got knocked out of alignment. There realy isnt any way i know of to adjust axial alignment on the rear of these bikes like you describe. Does the brake bind up bad? Becouse if its a problem with the wheel/ axle the brake will be afected big time as well. If its not the then check the torque on the rear sprocket (49 ft lb). If that doesnt fix it then pull the rear sprocket. Lay it on a flat surface and a put a stright edge acrost the top. If it wont lay flat that could be your problem. Theres a limit of just a few thousandths of an inch of warp.

 

Im having the same problem but, I found I was missing the spacer that touches the big inside long spacer.
I have no clue how long it has been like that but it tore up the oil seal. So I have a spacer and seal coming in asap.

It's actually kind of fun working on a bike.