as I noted in my OP, a major major headache is how to deal with CPAN modules the app needs. If the webapp was on CPAN, I could just make a makefile or Build script that says, "Hey, these are required, so go and get 'em".
That's maybe 80% of my wanting on CPAN. As for the rest of the installation of the program, it could be as easy as a small perl script that moves the appropriate files, to the appropriate places (say into the public_html of the account you're installing into) and then a little message that says, "To finish the installation, visit $some_url in your web browser" and we're done .
The other large issue is the testing suite for the webapp is almost never used outside of myself.
There's some other interesting issues that I think CPAN will help out, many to do with diversification of Perl, etc, etc.