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I'm afraid neither your "expected output file" nor the solution proposed meet your verbal specification of what you need. Why, for instance, does the first line read J6.A1 in lieu of J6.4 (taken from...

First off: You can do all that in a single sed and forego the whole script as well as the half dozen temporary files:

sed -n '/CONNECTIONS$/,/DEVICES/ {
s/"//g
...

Try
sed -e '0,/! IPG:/{/! IPG:/a\
\

testplan generation off' -e '; }; /! IPG:/ b;' -e 's/;/; permanent,/; t;' -e '/^ *$/!s/$/; permanent/' file

The s/ / / do the substitutions.
If you want to not have substitions for a certain string, then branch to the Loop before, i.e. have another line
/boards /bLoop
(If boards is found then branch...

The following has got some more fixes, e.g. it allows the PROBES sections to be last, and would even handle two PROBES sections.
awk '
NR==FNR {nodes[$1]; next}
NF>1 && $1=="NODE" {node=$2;...