Regarding the method 2, I have never worked with ds.surface, but looking at yt wiki I’m not sure it is what you need here. As a sanity check, I asked to print cylindrical_z of disk_upper_surf cells, and I think it’s all zeros, since I never got printed anything:

So with ds.surface you select exactly the planar cells. 

The way I usually select data is with include_above/include_below:

Could you please check if it works? Then you I think it would be good to compare the results method 1 and method 2 give on exactly the same data selection, so mass_flux = np.sum(disk_upper_surf[‘density'], ...)

Finally, I haven’t used calculate_flux either, frankly, I didn’t know it even existed. Again, from the wiki it’s not quite clear how it works, especially if you’re interested in the flux specifically from velocity_z, not from all the velocities. Here is my (probably overly complicated) solution to this problem that I often use in my work:

The idea here here is that mass flux is sum(m * v_z) / z

So I first create a new cell type that is momentum p = m * v. inflow and outflow allow me to get negative and positive mass flux values separately, which I do with mass_outf and mass_outf, where height is the vertical height, which in your case is 2.02 kpc (from 0 to the height in your my_disk definition). Btw, why is it 2.02 not just 2?

Mass flux is then simply mass_inf + mass_outf