from the factory they should have a properly aligned rear wheel. if you change where the adjusters are screwed into (you pretty much have to in order to change sprockets/chain) then its possible that its not set back correctly. you can use two very long straight edges lined up with the rear wheel to check, some people use string. i just kinda look down the back wheel and the chain and make sure the chain is straight. if the wheel is straight but the chain is totally crooked, the horizontal spacing of your rear sprocket/wheel might be off. one time i rebuilt the 250 bottom end but accidentally spaced the output shaft incorrectly so the offset between the small drive pinion and the large back sprocket was totally out of alignment.
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