That old floor certainly still has a lot of wood left on it. All of the frame mount holes in the sills are there enough to confirm it's fit. I think I would trust that for accuracy. The other thing I would want to confirm is whether the front doors would fit the space when the body sides are in place. The cowl only mounts one way so that may confirm distance from the cowl A pillar to the rear of the body. I always use the frame to fit things up after I've made sure it's straight and square. I can only assume that your body is on the frame from the photos.
I don't know how much was left of the original sidewall wood members but they would have helped some. I wouldn't be surprised about wood kit members being long. They would let the installer do the fit up of those and there could be some variation but I agree that it likely wouldn't be a whole inch but nothing surprises me much anymore. It looks like the rear of the sills had some rot but I can't tell how much. If there are signs left of placement locations then it would still have to be guesstimated a bit.
The drop floor bodys were similar but most of the difference was in the back end there. It makes me wonder if some of the wood was the same or not between the two.
I don't know if this will help or not:
http://classiccardb.com/ford/382106-...t-engine-.html