A quick question about the settings on the 5D3 - I have never MA'd a camera as I am coming from the 40D. Do I get a short and long MA reading for each lens? If so, if I test four focal lengths for a lens such as the 24-105, which suggested readings would I use? Or do you just average them out?
With the 5DIII and 1D X, you can enter separate wide and tele values for zoom lenses (primes, and older bodies with AFMA, one value per lens).
I test at intermediate focal lengths, too, which lets me evaluate performance across the zoom range - I usually do a test for every 'x' of zoom, e.g. the 24-105 is a 4x lens, so I test the ends and two points in between (I 'cheat' on the 28-300, and only test 5 focal lengths for that 11x zoom). Testing at 25x and 50x focal length distances helps me to adjust for the distances at which I shoot, and account for DoF at different distances. It's more work - but picking a value is basically a compromise, since most people shoot at different distances and for zooms different focal lengths, and more data mean a better compromise.
An example: for the 24-105mm on my 1D X, I tested 24, 50, 85, and 105mm, each at 50x and 25x distance. At 50x, the results were +2, +5, +3 and +2, respectively. At 25x, they were +4, +4, +4, and +2. Had I done both ends at 50x as recommended, I'd have +2 for both. I chose +4 for wide and +2 for tele, because of the +5/+4 at 50mm and because 50x distance at 24mm f/4 has a very deep DoF so I give more weight to the 25x value.
NOTE: at intermediate focal lengths on a zoom, the camera does a simple linear regression between the W and T values to determine the AFMA to apply. If testing intermediate focal lengths, you should set both W and T to the AFMA value you're testing.