Folks who are interested in this topic will get a lot of detailed info from the "Early 1928s" supplement to the JS. According to the supplement, the first 200 cars produced were never intended for sale (based on engineering notes I think it was originally 100 and then changed to 200). They were sort of demo cars meant to be sent around to important stakeholders, shown to the media, etc., and then
returned to Ford.
Many of the features noted on the prototype, such as the muffler clamp and odd shock arrangement, are also present on these first 200 cars. The JS describes many of these features. The flywheel-mounted timing pin is also found on some
early Canadian export cars, along with the FAM motor mounts.
Other than the distinct body dimensions and other changes in the sheet metal, I'm not sure how many of the differences folks are seeing on the prototype are specific to it, rather than just to the first 200 cars.