Do you have a (small) anonymized PDF sample we can look at? Is the PDF text even searchable and selectable in a PDF viewer?

At $WORK I use pdftohtml with the following command line: pdftohtml.exe -xml -stdout -zoom 1.4 [PDF FILE]

This will rip out all the text elements into an XML file with attributes for the font, x/y position on the page and text length. (-zoom 1.4 makes the positioning units 100 dpi, -stdout streams the output to STDOUT instead of writing it to a file).

Here is an example of what I typically work with:

<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE pdf2xml SYSTEM "pdf2xml.dtd">

<pdf2xml> 
<page number="1" position="absolute" top="0" left="0" height="1100" wi
+dth="850">
    <fontspec id="0" size="17" family="Times" color="#000000"/>
 <text top="103" left="115" width="602" height="18" font="0">XXXXXXXXX
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</text>
 <text top="120" left="115" width="602" height="18" font="0">XXXXXXXXX
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</text>
 <text top="186" left="115" width="103" height="18" font="0">ROUTE TO:
+</text>
 <text top="186" left="265" width="107" height="17" font="0">Audit Bil
+ling</text>
 <text top="220" left="115" width="128" height="18" font="0">SORT GROU
+P:</text>
 <text top="220" left="265" width="152" height="18" font="0">Invoice S
+ort Group</text>
 <text top="286" left="115" width="260" height="18" font="0">OH_GOD_IT
+_BURNS 2013-12-20</text>
 <text top="286" left="415" width="71" height="18" font="0">23:53:04</
+text>
 <text top="286" left="545" width="108" height="18" font="0">FOOBAR</t
+ext>
 <text top="320" left="115" width="602" height="18" font="0">XXXXXXXXX
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</text>
 <text top="336" left="115" width="602" height="18" font="0">XXXXXXXXX
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</text>
</page>
/<pdf2html>
[download]

I can then use XML::Twig with XPath expressions to pull the exact xml nodes I want:

open (my $XML, "-|", "pdftohtml.exe -xml -zoom 1.4 -stdout $PDF_FILE")
+ or die "$!\n$^E";

    # We are only interested in the text for the "ROUTE TO:" and "SORT
+ GROUP:" sections
    # Set the twig_handlers to extract the <text> nodes of interest; a
+ll other nodes will be ignored
    # XPath queries provide an extra 1/20 inch padding on all sides to
+ take font and rendering variations into account
    my $t = XML::Twig->new(
        twig_handlers => {
            '//text[(@top >= 180 and @top <= 190) and (@left >= 100 an
+d @left <= 111)]' => \&RouteTo,
            '//text[(@top >= 215 and @top <= 225) and (@left >= 260 an
+d @left <= 270)]' => \&InvoiceSort,
        },
        comments     => 'drop',  # remove any comments
        empty_tags   => 'normal',# empty tags = <tag/>
    );
    
    $t->parse($XML);
    $t->purge;
    
    close $XML;
[download]