You will use winmerge on files in your template folders, principally. But you'll use it on all files once first.
First, check the changelog in the new fileset; if any of the files you have overridden have been changed, you will need to use winmerge on the previous and new versions to find out exactly what was changed. Make good notes including line numbers.
Any of your override files that are not in the changelog can just be copied directly to the new installation's custom template folders (you will have to make all the custom folders in the new install.)
Here is the only tricky part: for any of your files in the changelog, use winmerge on your custom file vs. the new default file. Copy all of your changes to the new file, and save it to your new custom folder (important). If any line you changed was also changed from the previous to new versions (check your notes), you will have to carefully reconcile the changes. You will have to know what you are doing in this case - it can't be automatic.
Good luck, and remember - no mistakes are fatal if you have good backups.