I just did this with a new Alfine.. the key was to make sure the barrel aduster was out a few turns incase I made the cable a bit too tight. Did you see this page by chance? http://sheldonbrown.com/nexus-mech.html#cableinstall

I just measured 101 mm as shown in the pic there then cliped the stopper piece in (at this point the cable was not aligned yet) Then I push the pully down to give slack and put the cable in the correct spot on the joint.. then I put the cable end into the arm of the joint. I was off by about a mm but the barrel adjuster took care of that.

Also make sure you are in 1st gear when doing the actual work, I just flip into 4th to test the alignment.