Start by converting the content of your template files to UTF8:
    for i in `ls -R *.tex`; do iconv -f ISO-8859-1 -t UTF8 $i -o UTF8-$i; done
You can now move the new UTF8-template files into another folder:
    mkdir utf8
    mv UTF8-* utf8
Then navigate into the new folder and remove the "UTF8-" part of the file names:
    for file in UTF8-*; do mv "$file" "${file:5}"; done
As a last step you need to exchange the call for "latin1" packages to "utf8" packages instead:
    find -type f -exec sed -i 's/latin1/utf8/g' {} \;
That's it!