I put a wooden foot rule on the floor. The lens on a tripod, about 3 meters away. DOF was about 1 cm.
Now I did focus on one line e.g. at 20 centimeter.
If I had $1 for every time I've read about someone using that 'method' I'd probably have a 300/2.8 II to go along with my 600/4 II.
Here's the thing - the AF system is going to lock onto the feature of highest contrast at the correct orientation under the selected AF point. Note that the actual AF point is larger than the little box representing it in the VF (even with Spot AF, it's still slightly larger, although you should not use Spot AF for AFMA). So, you
know that you intended to focus on the thin 20cm mark running horizontally, but your camera saw the higher-contrast feature running vertically across the point - the edge of the ruler. That feature extends away from the camera, and anywhere along that edge would be 'correct' for the AF system. No wonder your AFMA 'made things worse'. That's why the commercial tools use a flat target oriented parallel to the image plane. Also, you were far too close - AFMA should be done at 25-50x the focal length of the lens.
The best test to see if AFMA is the solution is what AlanF alluded to a few posts back - set up on a tripod, with a flat, high contrast target (a sheet of newspaper taped to a wall, for example). Activate Live View, and take several shots using Live AF each time (not Quick AF - you should not hear the mirror flip during AF, you want to be using contrast detect AF where the CMOS image sensor is used to focus). Then, turn off Live View and take several shots with 'normal' (phase detect) AF. If the Live View shots are sharp and the regular AF shots are not, AFMA should fix that (and I really do recommend Reikan FoCal, in that case). If the Live View shots are soft, it's likely a problem with the lens, probably meaning a trip to Canon Service.
Hope that helps...