I fixed the side clearence problem. It was simple, I just loosened the two allens on the left side (from the driver seat) and applyed a little pressure outwards with a screwdriver. I found out that the left fork was too far inwards by going to the dealer and looking at one on the floor.It was clear that my axel was sticking out to far.
My fender still does not fit though as I don't have enough height with the speedmaster fender.
I have found a fender at a local chopper shop that will work and they can make the necessary mods.
