A few random suggestions after skimming your code:

• Prefer lower case for variable names (your code looks like it's shouting).
• Learn Perl here documents.
• Spend more time choosing good names (descriptive, explanatory, consistent, regular, ... spelt-correctly ;-).
• Your main program is way too long. Decompose it into modules. Write unit tests for each module. Avoid big-arse functions.
• Run your script through Perl::Critic.
• Prefer three-argument open.
• Insert $! in your error strings when a Perl function fails.
• Prefer low precedence or to ||; for example, prefer or die to || die.
• Don't use a leading & when calling functions.
• Avoid C-style for loops. For example, prefer for my $item (@arr) {...$item...} to for(my $I=0;$I<@ARR;$I++) {...$ARR[$I]...}.
• Prefer my variables to our variables. Declare variables at point of first use (do not declare a huge bunch of variables at the top of a subroutine). Minimize variable scope. Avoid global variables.

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