Since the diferential project Will hold up until I receive the parts donor (ir have to buy new ones), i Will continue all the other tasks.
Started cleaning the top of the gearbox and this round cover has two tiny holes: can I remove it and get a replacement?

That's a breather, it lets excess air out through that hole. Just paint it up, it's fine. But you can swap to the military version with a proper breather if you want.