Well, I hope someone can explain these results. I did screenshots of the reports at the peek AFMA value so you can see the images side-by-side that are giving the QoF. You can see the extra light in the report, and shutter speed. What you can't see is the heavy weight hanging on the tripod, tripod on basement floor (cement), central heat shut off (no vibration), tripod legs forced into wider spread at floor to reduce wobble, target on solid wall, target larger and of much better print quality, FoCal delay after mirror lock increased to 3 seconds, more time waiting after each AFMA change on body before continuing.
400mm and 140mm were done at almost same distance of 10.1 - 10.3 meters, I didn't have room to get any further away so the new 560mm was done at 10.1m where as the original was done at 13m.
It made sense to see the 400mm QoF increase (though I had hoped for more), but then I was puzzled to see a reduction of QoF at 560mm, and then essentially no change at 140mm.
The one thing I wonder, does FoCal use the declared target size (and hence calculated distance) as a part of the calculation of the QoF? I assumed having the target size increase from 116mm to 209mm would have improved the QoF because of the improved image captured, but maybe it's accounted for?
EDIT - left image is the new (better technique) attempt in each focal length below.