They buzz at 1 and 2 and are good until about 10-14. I know everyone is gonna jump on the 'Truss rod adjustment' tip, but the neck is perfectly straight. If anything it bows in the OTHER direction. I'll add photos when I get home from work. I did look at the nut and it seems fine to me. Like I said, i have 4 other basses set up almost the same way and they are fine. Who knows, maybe it is the nut.
I think everyone needs to know how to set up their own bass and you have to start somewhere. However, you are doing everything opposite to what you are wanting to result. I believe you need to try what others have stated - loosen truss rod and lower saddles. It's not the nut causing a third fret buzz.
I suggest GTS Google that s**t before touching another wrench.
Filing first 3 frets is horrible advice.
I'm sure you'll figure it out.