Whatever you do, please don't consider using a variable as a variable name.

Instead you should look at complex data structures like arrays of arrays. See perlreftut, perllol and perldsc for details.

Code review notes follow:

opendir (*LOWEST, "$input_directory_lowest")
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Please take another look at the documentation for opendir. You are still getting it wrong. You pass it the name of a directory handle (LOWEST) not a typeglob (*LOWEST). And there is no need to quote the variable $input_directory_lowest.

if ($do_I_pick_up_request == 'Y')
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And how many times have people tried to explain the difference between string and numeric comparison operators to you?