I don't think it's a nut or fret issue. When I hold the bass up, point the headstock towards the light, close one eye, & look down the neck on the low side... there is a noticeable dip that goes from the N/B joint to the 12th fret. I don't see it on the high side. As I climb the neck fretting notes... the buzz appears on the E and A strings as I get closer to the 12th. I've seen it, and dealt with it before. It's not so bad that I can't play it. I'll just hafta spend some time on it, and settle for less-than-perfect action.
<edit>
The nut
is janky. E,A, & D aren't cut deep enough. G seems ok (weird

)