Just do this...
  1. Download and install WinMerge (since it's the free one)
  2. Download latest version of Zen Cart
  3. Download your store from your server
  4. Place both stores in the same folder somewhere on your computer
  5. Highlight both folders, choose "WinMerge" from the context (right-click) menu
  6. Start probing around to see what it does

Many, many of your concerns will be addressed simply in starting the process. If you're like me,, you'll eventually have one of those "ah-ha!" moments as you begin comparing and merging files.