I was just thinking that maybe when you put the AAL in, you might not have put the axle where it was. When we did mine we did one side at a time and I think we took off the shock so we get a little more wiggle room.
When I brought mine in for the alignment the guy never mentioned about the back being out. Just the front and asked if I cranked my bars.
If the back was out wouldn't it dog track or you'd feel the vibrations of the axle being off?