I couldn't find almost any tutorials on how to disassemble or service this particular eBike motor (Bafang M400), so I just started removing screws and pulling out parts while taking a ton of pictures.
I found two dirty, rusty bearings that I cleaned and re-greased, along with all the gears, and then put it back together. Not only did I manage to avoid breaking it, but the noise seems to be gone as well. This was by far the most intimidating bike repair I've done so far. I've serviced every other part before, but I hadn't dared to touch the motor until now.
It also turns out that the motor is much better sealed than I expected, so I'll happily continue doing deep river crossings with the motor half submerged in the future, just as I have done until now.
Trial and error lol. Along the year i know how to do it by feel and translate that to torque wrench, granted i do mostly japanese and local(malaysian) car so things that required exact torque to function is very rare, things just need to bolted down and not strip off or came loose.