> cat CPV-ThreeNone-Output.txt | more [and remove the intervening rows & trailing dots with LibreOffice Calc]

I do not think you realize how much time of your life you could save by seriously learning (say for ~10 hours) GNU's text-processing commands. I understand you want to remove a dot per line if it is its last character:
$ sed 's/\.$//' CPV-ThreeNone-Output.txt

I do not know what you call an "intervening row".

cat CPV-joined-TwoCols.txt [the two fields are separated by spaces; tabs would be better]

Same remark as above:
$ tr -s ' ' '\t' < CPV-joined-TwoCols.txt
(If the separator is always one single space, the option -s is useless.)

Will someone tell me how the "join" output has its columns reversed respective to the target table ?

There is no "target table" in a join.

The "man join" page tells me that...

The man pages of the GNU commands are incomplete specifications. As written at the end of 'man join', you want to read 'info join'. In this case, you want to read about join's -o option, which allows to specify its output format. The 'info' pages are not only more complete, they are also more user-friendly (more explanations, examples, etc.).

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