Since you have the site backed up, you can probably go ahead and do the upgrade directly. I suggest you create a template of your own to make updates/upgrades easier in future. You can always either copy the files you modified into other folders OR rename the existing folders to something else. The second option may sound easier, but you'll end up with tons of files you didn't modify and don't need duplicated. Programs like WinMerge and Beyond Compare will help you compare your template files to the latest version so your template stays in step.
I made this list while creating a prototype cart for someone just to keep track of what files I changed. I'm including it here to give you a general idea of where you should look for your changes.
To create a very basic custom template (you can build from there), you need:
- includes/languages/YOUR_TEMPLATE/english.php
- includes/languages/english/YOUR_TEMPLATE/index.php
- includes/languages/english/YOUR_TEMPLATE/meta_tags.php
- includes/languages/english/YOUR_TEMPLATE/header.php (to change the logo)
- includes/templates/YOUR_TEMPLATE/template_info.php
- includes/templates/YOUR_TEMPLATE/common/tpl_header.php
- includes/templates/YOUR_TEMPLATE/common/tpl_footer.php
- includes/templates/YOUR_TEMPLATE/images/logo.gif
- includes/templates/YOUR_TEMPLATE/css/stylesheet.css
Anywhere you see a /classic/ folder, you can create a folder for your custom template. You can copy the necessary files from either the /classic/ folder, the /template_default/ folder or the parent folder.
Edit includes/templates/YOUR_TEMPLATE/template_info.php to give your template identifying information so you'll recognize it in the admin under tools->template selection.
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