I tried to output the chomped text to a txt file. When I open that text file in a text editor it shows weird overlapping text (like some sort of graphical problem).   [from this; emphasis added]

afoken has already covered the cross-system line-end mismatch and chomp problems pretty well. Here's a further example:

c:\@Work\Perl\monks>perl -wMstrict -MData::Dump -le
"dd $/;
 ;;
 my $s = qq{abc\r\n};
 chomp $s;
 dd $s;
 ;;
 my @lines = (qq{Overlapping\r\n}, qq{Strange\r\n}, qq{Text\r\n});
 dd \@lines;
 ;;
 chomp @lines;
 dd \@lines;
 ;;
 my $line = join '', @lines;
 dd $line;
 ;;
 print qq{$line};
"
"\n"

"abc\r"

["Overlapping\r\n", "Strange\r\n", "Text\r\n"]

["Overlapping\r", "Strange\r", "Text\r"]

"Overlapping\rStrange\rText\r"

Textngeping
[download]

The other thing that occurs to me is that your original file has "invisible" whitespace characters other than the  \r \n line-enders: spaces, tabs, etc. If these exist at the end of a line, it will cause a problem. Try something like (untested):
    open my $filehandle, '<', ... or die "...: $!";
    ...
    my $content = do { local $/;  <$filehandle>; };
    $content =~ tr{\x20\t\f\r\n}{}d;

In general, processing a file of a few hundred megabytes entirely held in memory should not be a big problem, depending on what you're doing, and you're basic approach (insofar as I can understand what it is) looks ok to me.

And, of course, the golden rule: Know Your Data!

Update: BTW:  my $content = do { local $/;  <$filehandle>; }; is the "file slurp" idiom; it does a raw read of the entire file to a string.

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