Also, I think that for the purpose of measuring for kilt jackets, we will want to wear a kilt and a shirt or sweater to take the measurements. That way, we will know what the actual measurement is over the clothes that are to be worn.
Don't do this. Clothing could add bulk to places where you need good fit. If your goal is to get something that fits bodies outside the 'norm', then measuring over clothing that would generally not be custom-made will distort your true measurements.

What you should do is take your actual body measurements, then add ease to those measurements. If you want your jacket to fit over bulky garments, then by all means measure the body wearing them, but use the difference of the body measurements and the clothing measurement as the ease to be added to the body measurements.

About the fell line. I don't think you really need to be exact when drafting the pattern. Do the 1/3 fell calculation that Barb gives you as a rough basis (minus the 2" rise). Add a couple inches or so to that measurement and when you try on your first trial jacket, put your kilt on at the same time. Mark where your fell is (or the average fell of those of you with more than one kilt) and use that as your measurement for your jacket. Lol, of course this assumes that your fell is in the right place, kinda like a chicken and egg thing now....

You could measure the kilt flat, but that assumes the person wearing it is wearing it at the waist that you used for your jacket. I know dancers that wear their kilts on their hip. Trying on insures both your jacket and kilt agree.