I did finally do it! I had a post describing how I did it, but it seems to be stuck somewhere or I didn't do it properly. I'll rewrite it if it doesn't come up soon.

Can anyone shed some wisdom on why my pod is displaying the way it is?

lib/Annovar
      -Examples.pod
      -Wrapper.pm

When I look at the main Annovar::Wrapper page, I get the pod from Examples.pod instead of the inline pod from Annovar::Wrapper.pm. https://metacpan.org/pod/Annovar::Wrapper

Any ideas for me?

Check that the NAME sections of your pod match their module name. MetaCPAN places a lot of importance on the NAME section.

For example Annovar/Examples.pod should contain the following NAME section:

=head1 NAME

Annovar::Examples - blah blah blah blah blah
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