Obviously, when one sees differences in the Assembly Manual, Shop Manual and MPC's, it does make one wonder.
Sorting out the various documents is certainly an interestng puzzle, especially because in many cases they don't tell the entire story. It's not a surprise that there are discrepancies, given that these documents originate in different organizations and over a wide span of time.
The assembly manuals as most of us have access to them are a snapshot of the assembly instructions that Ford's engineering department generated. The dates on the drawings range from early in the calendar year preceding the model year (example: '68 model year drawing generated in Jan '67) to several months into the model year. Some of the drawings are marked with revision history, so we know some things that changed, but we don't necessarily know how many times those changed, or if there were later drawings that were not available to reproduce. When Osborn put the manuals together, they were pieced together as best he could from surviving documents, and all of the drawings within a single manua were not necessarily active at the same time.
The shop manuals were prepared before the start of the model year, so they do not capture changes that occurred once the model year began. Also, some illustrations can be failry generic, showing "typical" part numbers for fasteners that may not have been the actual ones used in production.
The MPCs came later, so they have the benefit of hindsight. But, they serve a different purpose - they were not intended to instruct the assembly plant, their purpose was to provide replacement parts that were functional. Not identical, in many cases - they just needed to function. As time passed, improvements from newer model years would be applied, so some parts would be replaced with newer service parts. Sometimes parts were consolidated so dealers would not have to stock such a large variety of replacements (leaf springs, for example). At some point sales would drop off and parts would be obsoleted. And as all this was happening, errors crept in. I've found a number of instances where a wrong number was entered, some typos, and a few places where an obvious application for a given part was simply overlooked. By the time the final edition of the 65-72 MPC was published in May of '75, the first Mustangs were already ten years old!
The real kicker here is that no matter how much effort goes into the documentation, once production starts up things start to change. I forget who said "a battle plan is only good until the first shot is fired". In practice, there are problems with supply chains, sometimes things don't quite fit as planned or assemblilng in the intended order causes problems. Production operator skill levels vary from person to person, day to day. Sometimes they come up with ways to do things faster that are not quite the way engineering intended. Those differences show up between plants, and over time within each plant. So even when the documentation seems clear, we still have to double-check with what's actually been observed on vehicles. It can be very trying at times, but some of us enjoy the detective work, and getting info from other folks can be more rewarding than simply looking up a number in a book.
This really strayed off the original subject, but it's a fascinating subject and would make an interesting discussion in its own thread.