This is another awk version.
awk -f- <<\EOF data
FNR==1 { f = FILENAME".new" }
/Final structure in terms of initial Z-matrix:/ {
FS=","
while ( getline > 0 ) {
$1=$1
if ( $0 ~ /Variables:/ ) break
if ( $0 ~ /Variables:/ ) break$1=$1
print $0 > f
}
FS="="
while ( getline > 0 ) {
if( NF == 2 ) {
printf "%-5s%15.8f\n", $1, $2 > f
} else {
break
}
}
}
EOF