I'd suggest you fill the transmission with diesel fuel or kerosene and drive it around in all the gears for a half hour or so and then drain it again. That should get most of the crud out so you're not contaminating the new gear oil you put in. The only thing I now that will get all the water out is acetone, but that would get expensive to use as a flush , to say nothing of being extraordinarily flammable. I don't know if using a fuel de-watering additive would be of any benefit as they're mostly methanol which isn't miscible with the diesel fuel you'd be using as a flushing medium.