In the first script, you're opening your output files with:

open my $out_file3, '>', 'myoutputfilename6.txt' or die "$!"; 
open my $out_file4, '>', 'myoutputfilename7.txt' or die "$!";
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In your second script, you open your input file with:

open(FILE,'myoutputfilename4.txt');
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The input file name, in the second script, is not the same as either of the output files names in the first script.

Are you sure the second script is reading what you think it is?

If you do have the file names correct, then the next step would be to add a

as the first statement in the final while loop so you can see what is being read.