I don't get it either, MDodson. On my bike, the left fork has a hole the axle goes through and the nut, the right side has a bottom to the fork that bolts on, but the axle goes through the hole that's formed and bottoms out on a lip. You snug the bottom thing, torque the nut to spec, then tighten the nuts on the bottom of the fork. There's no alignment to do. Any cap on the axle is decorative only.


The OP's problem is most likely a stuck caliper, as 1screwloose said. Take it off, clean it up on the slide bolt things, put it together with some caliper grease, make sure it can freely travel back and forth.

 

Pads will be in tomorrow and I will be taking it apart for a closer look.

 

It is true that there is a fork alignment procedure for dual disc models.

Of course, it is imperative that the bottom slider be aligned with the stanchion.

But if we are to assume, and I think it would be fair to, that the fork (sideways position) is aligned correctly at manufacture when they calculated where the r/h/side bracket and caliper should go, then if you were to align the fork correctly, then the brake caliper, by default, would also be aligned.

Now, some models have a separate cap that goes on the bottom of the r/h for leg, to hold the fork in position, and to stop it from sliding sideways under lateral forces(for example, cornering). Others use a pinch bolt arrangement. Some actually clamp the wheel in between.

When the axle is installed, it can happen that the r/h fork leg is not aligned, which is why HD now use the hole in the axle as an alignment point. Indeed, on some models, the fender is sufficiently strong, that it can drag the fork slightly offline.

So fork alignment is necessary, and often overlooked.

I do not see it as the issue here though. More likely a poor service schedule, or workmanship, leading to one caliper being "lazy".

 

So I pulled the caliper that I thought had the prematured worn out brake puck and it turns out the side I thought was worn is still like new, it seems when all I could see was the part the puck goes in it loked like the puck was worn but turned out it was just seated deep into the caliper. I will be flushing out both calipers in the morning, I started on the right side thinking I should do the closest first but sure is taking some time.