We kind of focused on details on this site and as Jim offered that is a very wide area of study. Things like head markings on bolts, order of assembly, sealant products and application, direction of hardware installation, different suppliers (supplying slightly different looking parts) .......... are all examples of these details. As we like to say here - there are not allot of Easy buttons to press for most of the information or subjects covered here. Allot comes from the individual or combined efforts of our members, seeking to answer some unknown question or looking at an older understanding. Answers don't typically fall out of the sky
As far as I know there is no list of every difference between all of the 66's built at all the plants during every production period written. In some cases they are the same (much of the engine details for example) since those were not initially assembled at the car plant bu the supplying plant so you should only find differences in things applied at the car plant - possibly, accessories, alternators, air cleaners, decals. There would be more differences (for this example) from one month to the next.
Running changes took place at different times at different plants and over the last few years I've been posting surveys related to just 66 San Jose running changes. Try "66 San Jose running changes" in the search feature for some of these. Differences in paint, undercarriage, sealants and related subjects are peppered throughout many threads in this current section. Going to take some time for you to read through them.
Not sure your interest in the subject. If your looking to just understand the differences for general knowledge or if your working on a specific car. If your building a specific car as your goal it might be more important to focus on it but understand that the history and details are something many here enjoy just knowing/learning.
And before I forget - Welcome to the site. Hope you find the information and knowledge here helpful in your concours related projects and endeavors