1. Proof of authorship
Write it up and post to CPAN with or without PGP signature, or PGP sign and post to Usenet. :)
2. Control over distribution
This strategy is difficult to pursue and may not be in your best interests, due to above reasons and Perl being source code and often including components licensed under GPL or Artistic License. The best way is to work with honorable people, get them to agree to a no redistribution clause i.e. sold only for use on this site. This might (IANAL) conflict with work for hire law and also, most corporate clients want to own the thing. You can mention that you do allow redistribution but only under a separate agreement.
There are also installers that download from the net, you could require them to purchase first. And of course you can distribute a password protected zip file.. don't know who's doing this either.
Or, and I don't know anyone doing this, an powerpoint presentation on the PAR module IIRC suggested a case in which part or all of the module archive existed on a remote server for this purpose.
I don't know how much say commercial wordpress plugin developers make, but there it is, if you make a plugin to a web-viewable site then you can search for it with google.
There is also the strategy of setting yourself up as a trusted purveyor of an endless stream of information and extensions to the software, which will build revenue stream as well as making it more worthwhile for other participants to join in plugin development too.
Also you can be an ASP (application service provider). There is at least one perl based search engine company that makes money at this for what I consider isn't a great search engine even. This might be a good angle.
I think the best thing for you to do is write a short license agreement for your clients, consider going the CPAN route anyway, and then just put your copyright on it. Don't waste more time on it because it will just inconvenience potential users. I wouldn't buy crippleware that's for sure.
Finally you can sell with hardware, if it is a turnkey system. I once sold a perl based system to greatly extend and administer an open source C++ search engine. I got follow-on jobs to extend it after that because it worked well. But you have to support it then, hardware and all. You need to consider what your goal is and how you want to sell it (or if you do). I think if you are really creating some professional system that is well known the client will pay for it, especially if a live version is working on a major company's site.
If you are just interested in sharing your work but asserting your authorship, just put it in CPAN, signed or not. It will get looked at and it solves the main problems you mention. If it is great you can become a celebrity, write a book, get consulting jobs, and maybe get free flights and lodging at YAPC conventions around the world!