How would I take a screenshot with FIXED coordinates or window name and append the resulting image sequentially to the pages of a newly created PDF

Inside double-quotes, a * is a literal * character. To use it to match "any character except /" it must be outside of the double-quotes. Try these two commands in Terminal to see the difference:

ls "$HOME/Desktop/*"

...and:

ls "$HOME/Desktop/"*

So your command needs to be:

"/System/Library/Automator/Combine PDF Pages.action/Contents/MacOS/join" -o "$HOME/Documents/Dropbox/JL IMAC backup of important systems files/Natural Readers/Combined PDF.pdf" "$HOME/Documents/Dropbox/JL IMAC backup of important systems files/Natural Readers/"*.pdf

(I've tidied up the quoting/escaping a bit -- while you can mix-and-match double-quoted strings and \-escaping, it's easier to read and troubleshoot if you pick one or the other when you can.)

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Fantastic ! Works perfectly ! I am very grateful for your explanation and the solution.