You can accomplish what you need to get done using the appropriate variation on this one-liner:

perl -i.bak -pe "s/OrigTxt/SubsText/g" FileName1.txt FileName2.txt
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So, instead of the "s" commands being in a separate file, you could just have a bunch of one-liners in the file, each one specific to the substitution you need. Cleaner, and more maintainable. Let perl do the work for you.