The wheel alignment marks on the swingarm are pretty rough measures of alignment.
Use the old method with a long string (monofilament fish line is ideal). Set the bike on a stand, or get as vertical as you can get with the sidestand (watch out it doesn't go over!). I sometimes put the sidestand on a 2x4 block. Then wrap the string around the rear tire and rim once, toward the rear. Pull the two ends of the string to the front, put weights on each end (heavy enough to get the strings tight), and hang them over something like a toolbox. The string should only be contacting the bike at the rear of the rear tire, and at the front of the rear tire; no contact at the frame, sidestand, front tire, etc.; turn the front wheel straight so the string passes by on both sides. You want the string as high as possible while still not touching any frame or engine piece in order to get a more accurate measurement. Now get a flashlight and look closely at the two points of contact on each side of the front of the rear tire. Adjust the position where the weight hangs over the toolbox so that the string JUST BARELY contacts the front of the rear tire. Now you have the two string ends in parallel. Look at the front tire. Each string end should pass by the front tire (turn front so it is even) at equal distances. The distance should be equal on the left side, on the right side, and between left and right. If the latter is not equal, you have to loosen the rear axle and turn the adjusters until you get equal spacing up front (you have to re-adjust the weights each time). Once you get everything right, snug up the adjusters on both sides of the axle, and from that time on always make equal adjuster changes on both sides (by counting flats) so you never have to mess with the string again ideally...
Last edited by PaulBx; 11-01-2012 at 01:23 PM.