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cat -n starts from 1 with each file, so awk with its NR is better:
awk '{print (NR "\t" $0)}' input1.txt input2.txt ... | sort -k2,2 -k4,4 -k1,1 | cut -f2-Note: the awk inserts a tab-separated field...

If you want 12 output files you need to treat them separately, and a loop is appropriate.
for file in input1.txt input2.txt ...
do
cat -n "$file" | sort -k2,2 -k4,4 -k1,1 | cut -f2- >...

The result you get is exactly as specified - sorted by field 1 (all lines identical), then field 3. I don't see column 2 sorted - it's just random, as its results are unspecified. To keep the...

I dealt with something like this before. I had to add an extra column, which held the line number, like:

1 101 100 1
1 001 200 2
1 002 100 3

...so that I could give that column number to...