Is this on a fresh engine? I wouldn't think you would really need to change the CB oil unless it had a lot of hours on it? Just curious why you changed it? This thread is really long so I am a little uneducated to everything you have done. Sorry if this has all been covered already. I recently pulled part an 85 hour 951DI that the gear CB oil was still a clear light brown/honey color.
The hump your talking about where the oil sits between the gears will actually drain to the lower gear area because the engine sits at a 45 degree angle. Its just enough for it to run to the lower area. But I would think the problem is you can't really get to the bottom of all the oil sits to pull it out because the vent hole isn't positioned above the lowest point. I think seadoo positioned it towards the PTO side so its not in direct spray from the gears. This way its not as likely to push oil into the vent line as things expand. That just my guess tho.
In a perfect world, if the engine or boat was tipped 45 degrees clockwise, you could drain out all the oil because the vent would be at the lowest point. Then rotate it back & 45 degrees the other direction & you could put your 40ML of gear oil. Personally I would probably put 35ml in because 40ml is assuming all parts are fresh & clean with no oil added yet. I'm not too sure what would happen if you overfill it?
as far as the 45 degree thing, I am guessing tipping a sportster is pretty much out of the question......