One thing I see quickly is that your pass your hash of tokens into loadAndParse, but that function does not pass them to any other function, nor does it set the $self->{tokens} attribute. Basically, the rest of your functions have nothing to work on. I don't think this will solve all the problems though.

Update:
Also, in your new function, I believe you have your %tokens call defined incorrectly. It looks like you want $self->{tokens} to be a hash containing the token as the key, and it's replacement as it's value. You would need something like:

sub new {
  ...

  $self->{tokens} = \%tokens;

  ...
}
[download]

This would define the token attribute of $self to be a hashref containing your mapping of token names to token values. However, rather than relying on %tokens being defined globally, I would recommend that you pass it into either your constructor, or propagate it through your parseData function.

Update II:
You could also do away with the $self->{tokens} part of your module all together. The tokens are only used in one place throughout your module---the parseData function. So you could change the code to:

sub parseData($)
{
    my $self = shift;
    my ($data, %tokens) = @_;
    foreach my $match($data =~ /\%(\S+?)\%/g)
    {
        if($tokens{$match})
            { $data =~ s/%$match%/$tokens{$match}/g; }
        else
            { $data =~ s/%$match%//g; }
    }
    $debug .= "parseData has been run<br>";    
   
    return($data);
}
[download]

and change the loadAndParse function to:

sub loadAndParse($%)
{
    my $self = shift;
    my ($filename,%tokens) = @_;
    $data = loadFile($filename);
    $body = parseData($data, %tokens);
    $debug .= "parseData has been run<br>";    
   
    return($body);
}
[download]