Bash Script - File Comment out & Notate
No need to use quotes here, though it's not a problem:


useFile='deferred.php'
tempFile='/scripts/_inc/deferredTextTemplate.php'



On the other hand, it might be a good idea to double-quote $tempFile here:


newTop=$(head -n 15 $tempFile)
newBottom=$(tail -n 4 $tempFile)





It's hard to guess the meaning of the parameters $2 and $3 here:


changeFile () {

    ## Info About Action to be intered into File.
    workInfo="\n// Edited: $(date)\n// Directory: $2"
    logTag="$(date): [$3 @ $2]"



One way to improve that is to document them in a comment.
An even better way would be to reassign them to local variables with descriptive names.



The marker F8kR8ikBiF is buried deep within the script:


    if grep -q F8kR8ikBiF "$1"; ## Description: Does the file contain this marker?



It would be better to put it in a variable with a good name,
defined near the top of the script.



You were careful to double-quote most variables correctly, but not always:


orgFileCont=$(tail -n +2 $1 | sed -r 's/\/\*+ (.*) \*+\//\/\/ \1/')



You should double-quote the $1 there.

Also, the \/ make the expression hard to read. It would be better to use a different separator, for example ?:

... | sed -r 's?/\*+ (.*) \*+/?// \1?'




When you have an if-else block like this:


if [ -f "$1" ]
then
    # ... many many lines
    # ... many many lines
    # ... many many lines
else
    printf "%s File not found.\n" "$logTag"
fi



When there are too many lines in the middle,
it can be more readable to invert the if-else branches:

if [ ! -f "$1" ]
then
    printf "%s File not found.\n" "$logTag"
else
    # ... many many lines
    # ... many many lines
    # ... many many lines
fi