I can't help feeling there is something fundamentally inconsistent in your reply here and your response to fullermd. I'll grant that you know your client and your situation and you may be limited in your ability to explain your true requirements but... just food for thought.

You write, in reply to fullermd

The main security risk I can see is the possibility of an attacker copying my program (stealing a hard drive or system unit wouldn't work) and running it on his computer to gain access via a hole in the wall...I only need to delay an attacker a few hours and his attack becomes pointless. Though he can steal the program and run on it on his computer I am hoping he is unlikely to clone my users. I want to authenticate my system users with every pass of my program loop and shred my perlapps if any of various conditions

If security is so very important to your client, about the last thing you should be considering is an end-run around PAM. The more places security is defined, the more places changes to security protocols need to be updated, and the more long term problems. Also the more places you need to secure and protect from access. By adding a second authentication mechanism outside of PAM you are in fact increasing the number of potential attack vectors.

Second, modern versions of PAM support some pretty sophisticated user identification mechanisms, including bio-identification. Presumably, if those scripts are run on a personal computer, they have to log in at some point into the sensitive computer. I'm going to assume you are sophisticated enough to never ever put login information in the clear in your scripts, especially in a high security situation.

Why aren't you making your scripts owned by a user who can only be activated with a bio marker? Then it wouldn't matter what computer your would-be attacker ran the program on: when he tried to access the sensitive computer and reached the bio-security check, he'd be stopped dead in his tracks.

Third, if this is really so very important to your client and you really have no option but to run security checks before each and every operation, your client should be willing to provide a box with sufficient memory and CPU to handle the hit rate and security checks.

Forth, if stealing a disk won't work, how is it that these scripts are being stolen or copied in the first place? How is it that merely running the scripts on a personal computer would give someone access? That doesn't sound right at all. Have you considered front-ending the computer with these valuable scripts with a gateway computer that validates the users? Putting these scripts on a secure computer accessible only via the IP of that gateway computer or by an on-site login with bio-id? Limiting the actions those users can take?

Fifth, if your scripts can be stolen or copied, why wouldn't your user base be stolen or cloned? Seems to me that would be a much more direct way of cracking your system. Why wouldn't a serious attacker read your source code? I certainly wouldn't write off a script as not worth reading even if it contained only one line in it. Would you? I hope not. I'm not following your logic when it comes to likely cracker behavior.

Sixth, if security is essential to your client, should you even be using scripts for such sensitive operations? Might it not be wiser for both performance and security reasons to go with a compiled executable? With any scripting solution there is always a risk that an enterprising hacker can intentionally create and take advantage of time gaps between the launching of the Perl interpreter and the loading of your script to change the effective user id or wreck other havoc. If you must use scripts you might want to take a good hard look at the implementation and security checks done by Apache's mod_suexec.

Seventh, I question your logic that a pure Perl script hacking /etc/shadow would in fact be faster. If PAM is doing nothing more than a password check, my first guess is that it would be faster because you are using pre-parsed code compiled into machine code ops. With a script you have to parse and compile it with each run. Even if you are pre-loading modules and using signals or function calls for each user check, you'd still be running Perl OP codes which have to be translated into machine ops rather than machine ops. If PAM is doing more than a simple password check, then you aren't really doing a complete authentication if you by-pass PAM and as soon as your would be hacker figures that out, they'll find a backdoor through the things you aren't checking.

I don't know your situation, but based on what you've shared so far, it seems to me that you are trying to solve a problem with scripting that needs to be solved in a much more systemic way. I think you need to have a very serious talk with your client.