FoCal does a lot to tell you if your target is aligned properly with your camera/lens. It will also tell you if certain parameters such as the EV exposure of the target is too low. However, the software does not tell you everything you need to know to get the best results. You have to read and re-read both of the FoCal manuals to decipher that information.
I have run all FoCal tests with my D800...some of them up to four times with the same set of lens that you see listed below...with new targets and changes in lighting. I am just starting to really understand what environmental conditions and target conditions matter and which do not have much impact. Together, Pete other friends and I will figure what matters and hopefully let you know.
As to my own targets, I print them on the back side of thick photo paper because the back side is the matte finish the FoCal manul describes. However, I do the printing with my laser printer. One of the tests I plan to do on Saturday is to try a target printed with my wife's inject on regular paper to see if the printing really matters.
My conclusions so far is that a lot of these setup things matter in an absolute Quality of Focus (QoF) sense for the tests, but not in a relative sense. The AF fine tuning is comparing relative results to find the best AF fine tuning set point for a give lens. The Aperture Sharpness test shows you relative sharpness at each aperture for that lens. However, if I wanted to compare my test results with Pete's, then I have to start looking at the impacts of lighting, distance to target, white balance, etc on the highest QoF that I can get with my D800 with a given lens.