Actually every motorcycle H-D has made has had this issue. Bending the struts is how it is cured. Walk up to any Softail, Dyna or FL and stick your finger between the tire and the fender at the top of the curve of the fender and you will see the fender is always closer to the tire on the pulley (left) side.

Congrats on figuring out how to fix it for yourself!

 

The rear wheel is still centered in the fender after riding it, on the side stand, and on the floor jack. Nothing has changed or moved and it had nothing to do with being on the side stand or the rubber mounted engine. As I said, I checked isolator mounts and alignment substantially before I ever started to bend the rear struts. Mine was way off and over whether on the side stand or riding, not just a small flex tweek from being on the side stand or isolator mount flex. I knew customization was needed.
Anyway I'm happy now and can mark one more thing off my to do list for it.

 

spit beer through my nose on that one!!!
Good work, Eye-gore