Quote Originally Posted by isaiah36 View Post
The upgrade was from 1.3.7, which ran for a long time
The database-portion of the upgrade takes about 1 to 5 seconds to run. Anything more than that means there are some serious problems.
But the script you're talking about is probably doing more than that ... and probably doing it very poorly, if history is any indication.
See below:
Quote Originally Posted by isaiah36 View Post
it was executed by Cpanel/Fantastico built in script
oh geez -- that's the worst way to do an upgrade ... because it has no knowledge of any of your customizations, and simply blindly replaces your files with new ones. That's why winmerge now shows no differences ... because it wiped out all your customizations and your plugins.

A proper upgrade is done by hand: www.zen-cart.com/upgrade

Now you'll need to reconcile all database structure differences in every table by hand. And then manually fix every record that wasn't properly upgraded. Depending on the size of your database that could take a long time.
Or restore your site from the backup you made before upgrading and start over using correct upgrade steps.