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# /bin/bash
INFILE=input.txt

while IFS='' read -r LINE || [ -n "${LINE}" ]; do
    awk -F\| '{print $3, $4}' <<< "${LINE}"
done < <(tail -n +2 $INFILE)

Output:

 test2.txt      PROGRAM APPLICATION_SHORT_NAME="SQLGL" 
 test.txt       REQUEST_GROUP REQUEST_GROUP_NAME="Program Request Group" APPLICATION_SHORT_NAME="SQLGL"