Keep all your files.
But keep your data and your code separate.
Remove the code from your scripts because it doesn't belong. Remove everything before __DATA__.
Rename your .pl templates to .lat or .dat
Collapse any other page specific code needed into subroutines inside a module.
This is all that should be in your master script
use lib ...;
MyStuff::run_cgi( '/path/to/root/or/config/if/nonstandard' );
Eventually get inspired by https://metacpan.org/release/Template-TT2Site/tt2site and make the dynamically generated static parts of your site truly static
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