If all you are trying to do is to duplicate your current functional site, then do so. Copy the files from point A to point B. Then, modify the includes/configure.php nd admin/includes/configure.php to update the directory paths to reflect the new location.

Then as also suggested, copy your database from database A to database B. Go back to the configure.php files above and update the database information in both files.

Then run the cache update key program available for download in the plugins section.

Won't need to run the zc_install which propbably has a problem in this current environment.

As for maintainng "modifications", for a programmer this can be easily performed for the majority of changes. There are a few that may require detaled work to recreate or simply to load an updated version of the program that would be identified by code inspection. Old versions of ZC are available to which comparisons can be made to identify the applied differences. But as dbltoe suggested, in this case simply "starting over" or picking the features needed to support current business is a far better approach as it is faster and easier...

Also, upgrading "in place" is more difficult as there are file changes that have occurred that must be accounted for. Such as deletion of old files that are no longer used, but if left in place might cause issues or even security concerns.