I believe CPAN uses a custom pod2html generator or something similar. If you manually tweak the output of pod2html --css style.css to put the body text in class pod and the table of contents in class toc it should turn out better. You could also tweak the CSS instead if you wanted to.

For some reason, pod2html uses multiple pre tags for code examples, which causes it to look funny using the CPAN styles. If you make the code sections wrapped in only one pre tag, it should look like it does on CPAN.

Hope this helps.