Fire up
WinMerge and drag-and-drop your customized version of tpl_timeout_default.php onto WinMerge. Then drag-and-drop the template_default version of the same file into the "right" field that is now showing in WinMerge.
Click OK.
You'll see all the differences highlighted for you.
You can copy/paste from one file to the other, or even use the built-in controls to copy certain sections from right-to-left or vice-versa depending on what you need to accomplish.
Repeat with as many files as necessary for what you need to do.
When done merging the new pieces into your custom template file(s), be sure to upload the changes to your server.
You can also drag-and-drop entire folders into WinMerge in the same fashion. It will show you the differences of all files and folders and let you merge components as needed.
If you aren't running Windows, there are some alternative Diff tools besides WinMerge which you may find useful:
http://www.zen-cart.com/forum/showthread.php?t=7330
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