Looking at the Text::Diff module, I noticed the following:
my $diff = diff \&reader1,\&reader2;

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I assume that this means you can use a subroutine to return the column you need from the input files and then just use Text::Diff to compare.

Do you have some sample input files? What sort of output are you expecting to be generated (a list of the differences, print to screen etc) and what should the format of this output be??
Updated: Questions added

In reply to Re^3: Equality checking for strings AND numbers by rpanman
in thread Equality checking for strings AND numbers by Anonymous Monk

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