Hi Ben,
From bitter experience I strongly suggest that you don't attempt to drain the oil into two separate 3 litre jugs. 4 litres will come out, it will be too hot to put your fingers in, and it will come out real fast. The whole 4 litres takes under a minute to come out and if something goes wrong you'll have a hell of a mess. Been there, done that just recently.
I'd strongly suggest a single drain container of at least 6 litres to catch it all without spillage. I was using a 5 litre rectangular plastic bottle with one side cut out and even that filled up right near the top making it difficult to then pour it out through the spout without spillage. I then switched to a large plastic dish of around 6-8 litres similar looking to these:
That will catch all the oil without any going on the floor, because not only does it pour down from the drain plug some of the oil runs back along the gearbox and dribbles off from other locations, so you need a wide dish to catch it all.
If the dish has curved edges and isn't too full you can then easily pour the oil into a measuring jug without spilling it, or into a large funnel into a waste oil container to take to the dump.
Regarding the temperature of the oil, you don't usually have to drive the car to heat the gearbox up again after the new oil is added because all the metal in the gearbox is at the same temperature too and has tons of thermal mass so the new oil is quickly heated up to the same temperature once the oil starts flowing.
On the older style 4HP20 where the drain and level temperature is 80 degrees I find that if I get it up to about 85 degrees by the time I've drained and refilled the oil and started checking the level its dropped just a few degrees to 80.
I suggested low oil as a possibility as one forum member, I think it was Stempy had a similar groaning noise on his Xantia V6's gearbox which he found was low oil due to a banjo leak. After the leak was fixed and the oil topped up the problem went away.
Having just recently experienced a leaking banjo out of nowhere (but fortunately catching it quickly before any significant amount of oil was lost) I'd say its probably worth you checking for that as well - its in the front left wheel arch, if you put the suspension on maximum height and turn on full left lock you should be able to see the pipe that comes down from on top of the gearbox and goes into the side of the gearbox with a right angle joint and a bolt. If its nice and dry and dirty there its fine, but if it looks wet with oil around that area it needs attention ASAP. (refer to the picture in my thread

)
For level ground I'm not sure what you mean when you say the C5 auto levels - it won't adjust for the ground sloping, only for ride height! If you're parked on sloping ground the car will still be sloping. I should also add that when you're doing the final level checking the suspension should be at normal height - at maximum height the rear lifts more than the front (at least it does on a Xantia) thus tipping the car forward.
A couple more comments on the symptoms in your original post - when you accelerate from a standstill through 1st and 2nd it won't groan because the torque converter clutch is left unlocked in these conditions for maximum acceleration and pickup. Not only does this keep the revs above the "danger zone" where the groan occurs, the groan can only occur when the lock up clutch is engaged anyway, it never occurs when the clutch is disengaged.
If you then hold at a steady speed for a few seconds in 2nd the clutch will lock up (you may notice the rpm drop even though the road speed stays the same, or alternatively the road speed will increase while the rpm stays the same) once the clutch is locked (actually in controlled slip mode with a regulated 50 rpm slip) if you then slow down it will stay locked even as you slow down to 1500 rpm or so, then when you accelerate again it will be in its controlled slip mode and may shudder.
The kick that you're describing sounds a little bit like what mine is doing lately - if you're drifting with no throttle under certain conditions say around 30mph it will release the lock up clutch which lets the rpm drop to around 1000 or so effectively leaving you coasting, when you press the throttle the gearbox quickly re-applies the lock up clutch again, if this doesn't happen as smoothly as it should you'll notice a little kick or jolt where it feels like its suddenly engaging. I'm still investigating on mine to find out why its engaging so suddenly under these conditions.
One final thought about lock up clutch shudder, are you sure the engine is performing 100% ? Is there any possibility that you have an under load misfire or other engine performance issue ? Is there any hesitation or stumbling if you floor the throttle from idle in neutral, or when you suddenly press the acceleration while driving at low gear ?
I ask for a couple of reasons - one is that the pencil coils on the ES9J4S are apparently known for failing. They might not necessarily fail completely causing an obvious misfire at idle etc, but you may find that one cylinder is misfiring when you put your foot down hard.
The other reason I ask is that I've been thinking a lot about the engine/gearbox problems I've had in the last few months, and I've come to the conclusion that a poorly running engine especially an under load misfire causes a lot of problems for the gearbox and may even provoke clutch shudder and other weird symptoms like abrupt gear changes.
How ? One is that a misfire under load at low rpm will cause the power output from the engine to be "lumpy" instead of smooth, this may interfere with the gearboxes ability to regulate the controlled clutch slip.
The second point is that the engine ECU calculates an "estimated" torque figure in Nm based on RPM, throttle opening, MAP sensor reading, coolant temperature etc, and passes this figure to the gearbox ECU 100 times per second. The gearbox ECU uses this estimated torque figure as an important variable in calculating many things including line pressure, clutch engagement overlap, torque converter clutch pressure and so on.
My theory is that if you put your foot down suddenly and the engine ECU announces to the gearbox that its now putting out 200Nm of torque but due to a misfire or other poor running condition there is actually only 100Nm being put out, the gearbox operates the clutches in such a way that is expecting 200Nm which leads to poor quality shifts.
For example in the case where its needing to quickly engage the torque converter clutch in response to a sudden throttle opening if its expecting 200Nm it will apply a lot higher pressure to the clutch and more quickly than if it was only expecting 100Nm, if only 100Nm arrives but the pressure is high the clutch will grab abruptly instead of smoothly. I think that's what's happening with mine - the engine is reporting more torque than it's producing so the gearbox is reacting incorrectly.
The moral of the story is be sure that the engine is running smoothly and that you don't have any poor running symptoms or loss of power or it could be a contributor to the groan/shudder or to the rough engagement.