Those are mostly good questions, but the stall limiter question is a little insulting, so I'll ignore it.
All times were averaged over 3 trials, fuel burn was set to .00001. Turns were conducted at <100' asl, over the water. My procedure was to enter a sustained turn over the water do about 3 or 4 complete circles, or even more, in order to attain a sustained airspeed before starting the stopwatch at a point on the compass. I would do this test with different flap positions to find the optimal setting, and then conduct more tests with that setting to come up with an average.
In other words, I had already considered most of the variables that you are pointing out. As for different fuel % for aircraft with the largest gas tanks, that was an attempt to correct for a variable, not create one.
The specific version of AH I don't recall, but would be from within the last 9 months.