I don't think it is going to effect wheel alignment much if at all. When you put it together, if you can get the belt to run in the center of the pulley, you should be OK. The rear wheel is offset from the factory from the front anyway, and if you have a manual it will give you the measurements and tolerance. On my 99 Softail Custom it can be off 3/4" total from the front, and still be in spec. The offset factor on mine is .526" plus or minus .250". As you can see it is not to critical.

 

A possibility: One end of each spacer is chamfered. The chamfered ends must be installed facing away from the wheel, i.e. outward, and fit into a mated surface. Could be enough for the offset you are experiencing.

 

Now thats confusing; In my 99 manual it says that the chamfered ends go toward the bearing. Both front and rear. Did they change when they went to sealed ball bearings instead of the Timken roller bearings?

 

Do not agree with Jim Kraft's idea of just adding shim. This would bend the swing arms and they are meant to be square with
swing arm bearing bores. To just add a spacer could actually just spread the arms equally and in effect half the shift would be on the pulley side and you do not want that. (see attachment).
Also a attachment to clear up chamfers. Note instructions on large and small chamfer. (be warned there are so many variations over the years with Harley and aftermarket parts that who knows what correct. My bike's original spacers are just slight deburr chamfers with 2 drive notches on the edges for tooling purpose. I replaced them with home-made stainless spacers I made on a lathe.
Also a question for Jim Kraft. Were did you find the spec for the front to rear wheel offset? I'm always trying to tell people that the alignment of a rear wheel of a Harley is the bearing swing arm bores but most important the belt drive and that is has nothing to do with the front tire and I have never found the spec of this offset.

 

Yep. The 2000-2002 wheels are slightly different...of course...then change again in 2003. The 2000-2002 have sealed bearings for sure. The manual posting by grf000 is right on. Could easily be interpreted that largest spacer (right side) only has chamfer facing to the outside. This corresponds to the diagram if you look real closely. The manuals are sometimes not specific enough.

 

That is interesting about the chamfers. It does say that in my manual also.
But I don't have a factory rim and possibly factory spacers.

But before I increased the size of the one spacer I noticed the swingarm got squeezed down about 1/8" before everything made contact. That didnt seem right.

 

When you loosen the axle nut the arms spring out slightly but pretty much about the same on both sides. When Harley machines the bores for the swing arm they have it in a fixture that centers it and holds it with the wheel space at 9.625. For 1.500 and .500 spacers, 6.500 bearing hub spacing and the 1.125 brake caliper arm. This is what I have gathered from Softail

 

There again grf000; The offset may be different for different years, or maybe not at all. My 99 manual has it in the vehicle alignment section, where you take two straightedges on each side of the rear wheel that run to the front wheel. Then you measure the distance from both sides of the front wheel and subract the difference to get the amount of offset. Then they give you a table of what it should be within a tolerance of .250".

 

I thought I fixed it but the rotor still gets too hot after a ride. The pistons seem to open after releasing the brake. I guess the rotor still is not centered enough in the caliper. Any ideas?