Kingpin riders has a thread that discusses the same issues on a 2006 Kingpin. There isn't a post that shows the outcome but rear wheel alignment was suggested because you can't always trust the alignment marks. Here's a couple pastes explaining how the OP should check the alignment:
Make sure your back tire is straight don't trust the guide marks, jack it up and watch your belt on the rear sprocket when turning by hand the belt should run right down the middle and not to one side.
The best way I thought of to check the rear wheel for alignment is to measure the distance from the swingarm pivot rod center to the rear axle center on each side: make sure they are equal. I figure the rear axle absolutely has to be parallel with the pivot rod holding the swingarm to the bike frame. I probably ought to check the owner's manual on this one.
Retired USAF, IYAAYAS!
2008 V-Star 1100 Custom Bobber project
2011 Crimson XR with Forged Highway Bars / Hard Bags / Passenger Backrest, Ness parts including Smooth Layback Plate Frame/Mount / Rad 3 Mirror / deep cut grips / drivers floorboards /shifter peg / brake peg / passenger pegs. Witchdoctor black rack, Lloydz filter / timing wheel / VFC III, 7Jurock windshield, Drag Specialties seat.