Two things:
Is the easiest way to put a flat section on a 5mm motor shaft to use a dremel with a grinding attachment?
And
What size grub screw should I use in a pinion on a 5mm shaft?
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Two things:
Is the easiest way to put a flat section on a 5mm motor shaft to use a dremel with a grinding attachment?
And
What size grub screw should I use in a pinion on a 5mm shaft?
The easiest way would be use a milling machine. But your way would work, a file may give you a more consistant flat though. I would use a M4 grub screw maybe, it depends on how much material the pinion has ideally you need 1d (4mm of thread for a M4 screw).
5mm shaft, M3 setscrew.
Otherwise you need to file/grind the shaft to much down.
use some sort of threadlock and check them for tightness whenever possible as well.