Several things.
1. It looks as though you need to set the witness point at the zero fret. The E string seems to be forming a lazy arc over the zero fret rather than a clean break angle.
2. I disagree with having the zero fret higher than the others. If you were to place a capo at the first fret, it would then be the equivalent of a zero fret. It doesn't need to be higher than the second fret. So nor does the zero fret need to be higher than the first fret - it's just another fret. You might add a couple of thou to allow for some wear, but certainly not as much as 10 thou. A higher first zero fret will just create intonation issues in the first position.
3. To remove the nut, place a block of wood along the zero fret side of the nut and tap the block with a tack hammer toward the headstock. A light sharp tap will free the nut. If you don't want to remove the nut, use your sanding beam from side to side of the neck, keeping the beam parallel with the string path. If you are worried about scratching the inside face of the nut, put a couple of layers of masking tape on there first.
4. A fallaway in the upper frets is appropriate for an acoustic bass, not a solid body. On an acoustic bass the string tension tends to distort the top plate, pulling the neck forward and thus affecting the fingerboard extension that is attached to the body. It creates and upward angle of the fingerboard extension. A solid body bass does not have any part of the fretboard attached to the body, so this neck-to-body geometry does not affect the fretboard. No need for the fallaway compensation needed on acoustics.
5. If you are getting fret buzz in the upper frets, it's an indicator that the bridge is too low. And that raises questions about how you are doing your setups. How are you determining the amount of relief? How much relief do you have, and where on the neck are you measuring it?