Trying to follow along with this discussion. In part I think I might understand and can help, but then I don't seem to fully understand. If I've got this right let me know:
You setup a ZC site. You got excited and began changing things about how it is displayed to the point of almost completely the way you want it.
You then realized that, hey I should have been doing this stuff as a custom template instead of modifying all these things.
Now, you want to gather all of your "changes" into your "custom" template so that it all is grouped like it probably should have been to begin with...
Am I on the right track?
If so, the solution is rather straght forward, but could involve some time... If you never created some form of custom template folder, I would suggest doing that frst for all expected override folders in all locations. (There's a plugin that describes the template overrides.) Then pretty much everything that was in the classic folder(s) for all of those locations should be copied to the equivalent custom folder.
Then take a look/compare the changes made to your overrideable files and copy those files into the template override unless the file already exists (css is a little different, but to be addressed momentarily). If the file exists in the template override directory, then have to evaluate the contents/changes made. Technically if the "page" applicable to the file has been right all along, the changed file is probably useless because it isn't accessed.
Then need to look at what files are extra in the non-template override folder(s) to see if the extra file(s) should be put into the template directory at least for some consistency...
With all that done, then go back to the classic directory(ies) and restore them to the original "blank" state. Restore the overrideable files back to their original zc design. (Again though the css files are a bit different). Now at least all of the template files are in one place, except for the css... The reason to save the css files for discussion is because they do "all" load, but in a sequence, and the last one to set something wins... So, couple of ways to go about things depending on the css changes. Again though, compare the original file(s) to the modified version all discussing the template_defaults folder... Any "addition" made in the current file can be added to the top of your new template file in/under the same format. Anything that was taken away sort of has to be addressed/readdressed in the new template file... So either have to know what the "default" condition for that value is so that it can be "force" entered to override the default template, or hazard to modify the default template css and "live" with whatever it does to future templates...
Work for ya'? :)