... I really don't like the use of oil pumps as the bits you really want out of the way, pumps often don't pick up.
Yes, sometimes you get surprised with what comes out of the drain plug on old vehicles...Could it help by making sure the oil is a bit warm when changing (even on the gearbox)?

Maybe also (extremely carefully) attach a small magnet at the end of the "suction hose" to lift out whatever chip that shouldn´t be messing around in the box?