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If I understand you correctly, you want to specify the value to insert after DRIVES. Try this:

z="TEST"
grep -l '0007862454' ./* | xargs awk -v newDrive=$z '/DRIVES/{a=NR+1}...

Try this from within the directory your files are in:
grep -l '0007862454' ./* | xargs awk '/DRIVES/{a=NR+1} a==NR{$0=FILENAME}{print > FILENAME".new"}'

Unless I misunderstand you, there is no problem with committing directory trees into source control systems. If you want a structure of /mod1/files then you should just create it on your local file...

try this from within your folder with the links:
find . -type l | xargs ls -l | awk '{system("ln -sf " $11" "$9)}'

Although, you may want to test this first or it will mess up your links:
find ....

I think your file must have some control characters in it that are not visible and also not copied into your example text.
That would explain why the code works when I use it on the examples given....

No problem. It is better to make the code more readable:

awk '
/UDP flood/{ --> match lines with UDP flood
flood=$0; --> copy it for later
if(line){ ...

awk -F, '{a[$1]++} END{for(row in a) if(a[row]==1) print row}' file*

A bit messy, but:

awk -F, 'NR==1{print $1",OUT1,OUT2,OUT3";next}{b=substr($0,length($1)); print $1","gsub(/[12]/,"",b)","gsub(/[34]/,"",b)","gsub(/[56]/,"",b)}' file

path2=$(echo "$path" | sed -e 's/\//\\\//g')

sed -i 's/triumph and disaster must be treated same./follow excellence success will chase you./' file1