You caught me in between naps.

Oh, hold on. Time for another nap.
Rob
On another note, I wonder if the fact that you used a boot last is the reason you have the gaping between the facings, I would still like to see a photo of the top surface. Firstly the back of the last is probably a bit thicker than a shoe last and also the shape of the cone of the boot last is sometimes a bit more upright and thicker than a shoe last. When you last wet it is possible that the extra stretch available has allowed the gaping to happen. I don't see that the little slit in the lining is a weak spot, it really doesn't make a difference I don't think.
To restate what I think you are suggesting is; A way to take a scanned image into the program and overlay a geometric design on it. The user would then scale the geometric design so that the mean forme can be fitted to the standard. A user could select a style such as derby and this would define all the key points for the pattern itself.