how many of the link are you trying to line up?? just the 2 on the cam sprockets or all 3 including the bottom?
either way i have used Enthalpy's way of setting cam/chain time and time again and its worked every time for me..
http://rs-enthalpy.com/tuning/sr-cam-alignment.doc
the problem with lining up the links is.. you have no way of knowing how many times u gotta spin the motor to get them even close to lining up. If you have the front cover off it makes it a little bit easier.