Since my name was taken...surely not in vain
...I'll give my best shot at responding.
I think you are taking measurements in a pretty standard way although I do it a little differently, using a low and a high instep--corresponding roughly to Sabbage's section six and five, respectively. Look at the Sectionizer as it is applied to the foot rather than the last to get a clear and accurate idea of where these girths are taken.
Actually, Lance my short hell is measured from one section up the heel to section five...or the high instep. My long heel is measured from the same point on the heel to section six...or the low instep. I find that in a well balanced foot the short heel will be one and a half inches smaller than the long heel. But I don't go looking for that difference. It's simply there most of the time. Some feet will not be in that ideal proportion,of course, so again it's something to just be aware of and not striven for.
Measurements around the foot are sometimes different from around the last especially if you think you can hold the tape measure exactly the same. Plus, I use a tape measure on the foot and a dacron string on the last.
For instance, the ball measurement on the foot goes from joint to joint--a rough 15* angle; on the last these points can be located accurately so the measurement is taken pretty much from one joint mark to the other.
The waist is taken behind the joints at roughly the same angle and the last is pretty much the same except that the string just naturally finds the narrowest configuration unless you have built up the waist.
The low instep is taken over the middle cuniform, pretty much straight around the foot; on the last the low instep can be located with some accuracy on the dorsal surface of the cone using the spatial location of the middle cuniform as a reference point and the string crosses that mark but finds its own position under the last.
As for the high instep, the tape goes over the root of the fifth and between the middle cuniform and section four....on the foot. This would be section five. On the last, again, the high instep can be located on the top of the cone and the string goes over the mark and around the "cuboid" bump on the side of the last (assuming it has one).
Bear in mind that the empirical measurement of one section (let's assume, hpothetically, a size 9 foot and a section length of 2.4 cm) on a flat surface such as the pedograph will not translate to 2.4 ccm when it is transposed to the top surface of the cone. While each section may indeed be equidistant, a sectional distance of 2.4 cm on the horizontal baseline will probably increase to 2.6 cm (or more) between section marks on the dorsal surface. Remember, especially if you are making boots that Sabbage's Sectionizer postulates a shoe last with little or no heel. Whereas a boot last will generally have considerably more heel. Thionk of the Sectionizer as a two dimensional grid and then mentally superimpose the profile of the last on the grid--a very different look results, but to my mind still valid.
That's the way I do it...hope it helps...
PS...I reproduced Sabbage's Sectionizer from Golding as faithfully as I could (since then I've generated better illustrations) and it is pretty dern accurate. But I think that on modern lasts, the cone doesn't rise as far back toward the heel as Sabbage's illustration indicates--especially on spring loaded lasts. Practically speaking, what that means is that on my lasts, at least section four is in mid-air.
PSS...sorry this is so long. If someone else can explain it better shorter...have at it.