pop2pipe uses standard Net::POP3 Perl library. Unfortunately the library allows specifying neither alternate ports nor SSL protocol. The workaround is to use Mail::POP3Client library, however please keep in mind:
1) the library is not a part of standard Perl distribution and is not available with most shared hosting accounts
2) SSL connection requires additional libraries, that are usually not available for shared hosting customers.
As to posting code for customization of non open source software, I would suggest using diff utility:
http://en.wikipedia.org/wiki/Diff