Credit to tomt for the pic.
In the pic you can see how the bends on the left spokes are longer then the ones on the right, this allows all the spokes to be laced from the inside of the hub without any clashing issues.

 

You might have to true the wheel again. There is an offset on the disk side of the wheel. This will bring the spokes in so the caliper will fit. Check your manual in the wheel and truing section.


You will have to take the wheel to Harley or a bicycle shop. I took mine to a old school bicycle shop because they true wheels all day long. Bring your manual along. I went to three shops before I found one that would true my wheel. The shops with younger owners don't want to deal with it.


Why I did not go to Harley? I did, they told me no one there can true wheels because they replace wheels already assembled and trued.

 

Take that **** back to whoever you bought it from. It's incorrect.

I have had the same 21x3.5 with both my stock mid-glide setup and with Fat Bob (wide-glide) trees and no problems with brake clearance.

EDIT: Now that I'm thinking about it. I would still take it back but if you opted not to take the wheel back and/or fix the lacing issue, if you switch to Fat Bob trees, you would then use a rotor spacer for the new wider setup which would then allow the caliper plenty of the space behind it, even if you left the incorrect lacing job.

 

I agree that whoever laced did not do it correctly. The stock hubs are referred to as "inside lace" hubs. All the spokes should be on the inboard side of the hub.

 

I'm not sure about that. I do know that the stock 19" wheel has them all on the inside too.

 

That's where I learned how to do it, when I was a bicycle mechanic when I was a kid. It's really almost the same thing, whether bicycle or motorcycle.

I found that bicycle wheels are easier to lace up, because the spokes are flexible and you can "weave" them in and out. Motorcycle spokes are rigid and you can't do that.

On the other hand, bicycle wheels can be a bitch to true because the rims are kind of flimsy and go out of true if you look at them cross-eyed. Motorcycle wheels are pretty easy to true because the rims are so rigid, you have to work at it to get them really out of true.