I replaced a rear tire on a 05 fatboy and noticed the axle was cracked near threads, I installed new axle 41110-79A and it appears it is too short or the adjuster on the nut side has too large inside diameter. I can't line up adjuster on nut side to coinside with adjuster on the bolt side.
Does anybody have any input on the subject, I am baffled, The rotor and pulley seem to line up ok. Is the inside diameter on the axle adjusters the same size on both?

 

I ran into a similar situation while installing my new wheels. If you look at the axle it tapers down to the threads. Your adjuster may be resing on those and not the thicker part of the axle (where it needs to set). Try putting the axle nut on so it squishes the swing arm a little, not so tight that you can't move the axle with the adjusters. This should push the adjuster collars onto the part of the axle they need to sit on.

 

Don't forget the anti-seize!!