I haven't read through all the code yet, but small tip: use tr/// instead of s/// for single character substitutions.

    #Set common delimiter
    for (@lines2) { s/(\t|;)/\t/g }
    for (@rejects) { s/(\t|;)/\t/g }
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    #Set common delimiter
    tr/\t;/\t/ for @lines2, @rejects;
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