briandoakes:
Ok, so in short.. any thoughts on how to extract all of these customized core files and put them where they need to be?
A file compare program (WINMERGE) will give you a very quick LISTING of files in DIRECTORY "A" that are different from their comparative files in DIRECTORY "B"
In your case, your MODIFIED files are all likely to be in the main "includes" folder (not admin/includes)... just the main includes folder.
So...
In winmerge,
in the first location selector option... navigate to the location on your hard drive where you have FTP's your site to, and drill down to that "includes" folder
in the second location selector option... navigate to the location on your hard drive where you have unzipped the same version of ZC, and drill down to the "includes" folder.
Then do the comparison...
This will LIST all files that are UNCHANGED and CHANGED..
You can reasonably assume that all the CHANGED files are those customised by your developer.
It is likely that CHANGED files will appear in:
/includes/languages/
/includes/modules/
/includes/templates/
BUT THERE COULD BE OTHERS IN OTHER DIRECTORIES TOO...
These now need to be MOVED into a CUSTOM (over-ride) structure, that meets the directory arrangement of such override structure (viz: your "custom" template system.)
In effect, you will be EXTRACTING all CORE files that were edited, and will be putting them into their appropriate OVER-RIDE folder.
When you have extracted EVERY SINGLE FILE in this way - and MADE SURE they are in the proper override folder, you have the basis of your custom template.
Then.... you will be able to RESTORE the CORE system to the way it is meant to be... by overwriting it with the original files... it will be safe to do this now, because the customised files will be in their over-ride folders
(OVER-RIDE and CUSTOM folders essentially means the same thing).
You could then LOAD your "new" custom template in the same way that you would load any new template. Your site will be very confused at first as it is "expecting" certain settings. You will need to reset various settings - the first being the LAYOUT BOXES CONTROLLER RESET, and possibly several others in various admin areas.