First I echo Bob's feelings but lets work through the question in any case if for no other reason to demonstrate the process and thought process.
Agree the first step is to find one of the original buildsheets and get a Marti report to confirm the rear gearing though (see below) it is only a small part of the picture
How were the staggered rear shocks called out? I have an M code 70 mach 4 speed with what appears to be original staggered shocks. It also has an uncommon 3.91 traction-lok. I have seen a couple of other M code 4 speeds with 3.91 axles for sale but never found out if they had staggered rear shocks. I assume mine were a factory mistake but how can I document it?
The staggered rear shocks were not related (on cars typically offered with that option) the staggered rear shock feature.
You didn't list where the car was built? Did it come with a buck tag and if so what is stamped on it?
If after al the homework proving a factory oddity/screw up/or order change in the middle of a build is difficult. I would
1- Start by stripping as much away as possible
2- Documenting through pictures of the attachment of the panels related to the difference and all surrounding panels to rule up a clipped car
3- Collect and document the panel dates from all the rear panels
4- Have one or more disinterested third parties (hopefully with recognizable names in the hobby) view the unrestored car and ask them to write up their observations
Then your left with the choice of leaving it as is or altering what you found to what Ford intended to build.
Have been involved with dozens of these sort of issues and though interesting they can be a pain. And you have so many owners and builders that want to make their cars stand out (NOT suggesting this is the case in this discussion), create a story or somehow increase the value of the car it has case a shadow over those owners that have true mistake cars that are out there though very very rare.