All of my cameras came focused with shrink wrap around the barrel to prevent it from being accidently changed. For those that aren't, once the focus is set, I would either tape or shrink wrap it to not have to worry about it again.
Yes, the horizon adjustment is very important. There's one thing that you didn't mention that is very critical to proper alignment. After finding a good horizontal straight edge for calibration, you should allow the ball to hang over the edge of whatever the DF is sitting on and then let it settle because that's how the ball will actually be in flight. As you mentioned, very slight rotation of the camera in the ball is an exponential move to the image and so is the difference of the slight angle of the ball when resting on a surface and when hanging on it's own weight when floating. In other words don't calibrate the horizontal level while the ball is resting on a flat surface because it's not the camera's actual position while in flight. Once I have calibrated the level, I make a small mark on the foam and the ball housing and simply make sure those marks are aligned before each flight to ensure a good level horizon.
ORIGINAL: BB_DF
The four holes in the foam are obviously intended to accommodate some kind of tool for this purpose.
That's a good idea but those holes are actually for ventilation. The first generation camera ball did not have vent holes in the rear as it does now and the foam didn't have holes either. The problem was that the camera's circuit board was overheating inside the ball and causing the image to go static. I mean it got really hot and that's not good for the electronics or that foam because it is very flammable! I have noticed small pieces of charred and deformed foam in mine where the board sits.
You can easily make a shade for that monitor or get a professional one [link=http://www.hoodmanusa.com]here[/link]. For the best price, I would recommend getting it [link=http://www.bhphoto.com]here[/link]. I use these for all of my CRT, LCD monitors and my laptop.