That neck is bad ass! It looks to be a slab fretboard, so it's probably a '62 ri neck (as opposed to a '64 with the curved laminated board). If I'm not mistaken, I do believe the CS made a run of '62 Jazz Basses years ago (probably around '02 when this was made). Whether the white dots are normal for that neck, I don't know. My CS '64 has almost tan colored clay dots. I think clay can be porous though, like yours but mine are pretty smooth.
I can tell you that your decal looks just like my '64 CS from what I can tell from your pics. It's a pretty thick decal too, I can definitely feel the borders. I believe the CS would have used the same style decal on the '62s as the '64s.
Whatever the neck model is, it looks like a genuine CS neck to me. I'm not a CS expert, I'm just comparing it to mine.
Why do you think the truss rod has been repaired? Pics?
EDIT: Here's a pic of my C'64 headstock (made in '05)..