1. With a 50d, you only have one choice of focal length, so with your f2.8 fixed max aperture lens, use 55mm.
2. Here's an article I found interesting:
http://www.slrgear.com/articles/focus/focus.htm
The gist of it seems to be that there is a LOT of variability in the AF system.
3. Do you use mirror-lock-up and the 10-second timer for less camera movement?
4. I'd suggest much more light (or flash?) to have a much higher shutter speed to minimize camera movement.
5. You can't necessarily depend on the super-imposed AF point really using the "Focus here" point for focus. The DataColor and LensAlign devices have a more prominent, contrasty target that is to the side of the ruler.
6. My practice with a 50d and 5dm2 was to take pictures of a target on a large brick wall, outside with tripod and square to the wall, with micro-focus-adjustment values of -20, -15, -10, -5, 0, +5, +10, +15, +20 and go from there. All my lenses ended up fine with MFA 0.