I recommend #3 - a proper AFMA on all lenses. I use Reikan FoCal.
...or just use a piece of paper with suitable lines drawn on it.
There's no need to complicate basic AFMA tests, providing they're done carefully. You should probably put the camera on a tripod.
I've been getting the feeling round here recently that if you don't purcahse AFMA software to do the adjustments, you're as much of a "newbie", or even "simpleton" as people who only shoot JPEG and not RAW.
Doing them "carefully" is not so simple. For example, the commonly used printout where you focus on a horizontal line is designed for Nikon cameras. With many Canon cameras (including the 6D) that is not optimal because you're using an f/5.6 line on the AF sensor, and not a more accurate f/2.8 line.
I agree that purchasing AFMA software isn't required - but it makes it easier to get accurate results. The commercial tools (LensAlign, etc.) also make it easier, but IMO the software is even easier. If you use a DIY setup, it should recapitulate the features of a commercial tool (stable setup, 2D focus target parallel to the image sensor, angled ruler, etc.).
A 'piece of paper with suitable lines drawn on it' isn't the way to do it, IMO, as it can lead to incorrect results. Done properly, AFMA helps you get the sharpest images from your gear. Done improperly, it can be worse than doing nothing, and I suppose that's why Canon basically warns against doing it ('do it only if necessary, it might prevent correct focus from being achieved').