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Another approach, but more as an exercise because it lacks clarity:
awk '{p=$0; n=NF; for(i=3; i<=n ;i++) {$0=p; $i=x; $0=$0; $2=$2 " (-" i-2 ")"; print}}' file | sort -k3,3 -k1,2

Does the output order matter? Try awk ' {for (i=3; i<=NF; i++) {printf "%s", $1 FS $2 FS "(-"i-2")"
for (j=3; j<=NF; j++) if (i!=j) printf " %s",...