Ok, the evidence for problematic behavior is already evident from the equivalent bulk part. While the total energy converges (barely, and in very many steps), the density matrix actually does not converge!
Thus, your first goal is to stabilize the equivalent bulk run, or, as an alternative strategy, skip it completly and go directly to the two-probe calculation. For this, change line 376 in the input file to
initial_density_type = InitialDensityType.NeutralAtom
However, the real reason for the instability of the equivalent bulk run is most likely because the electrodes are too short. I would make them twice at long. At the same time, you probably do not need such a long central region, so you can keep the total size of the system fixed by removing 2 periods in the central part.
For safety, I would also increase the size of the XY unit cell to 25-30 Angstrom instead of the current 18. This doesn't really influence the stability, but it might leads to some inaccuracies in the results in the end.
Further steps towards better convergence would include reducing the mixing parameter (probably not necessary) and increasing the temperature to perhaps 1000 Kelvin.
But try to just increase the electrodes and the XY cell, and just rerun with current parameters as a first attempt. If that works, there's no reason to worry about the other things!