steph_bow,

If you're concerned that that the $_ variable is going to get clobbered, try reading/assigning each line into a variable, as in:

while (my $file_1_line = <INFILE>) {
   ... do stuff
}
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BTW, your code would be much more readable (to Perlmonks) if you only included the relevant code that demonstrates your particular issue. You might consider weeding it down to about 10-15 lines, with not so many comments, as they don't aid in increasing my understanding of the problem at hand.

Update: Added a number to the variable name