I'm working on some additions to an existing BLFS 8.2 system which should be using Linux-PAM-1.3.0 and Shadow-4.5. After installing these, I am unable to log in.

I have heeded the warning on the Shadow page to the letter, double-checking all of the configuration files from these two packages, and even recompiling both. I do notice, though, that the files in /etc/pam.d are all exactly one byte larger than the corresponding files in one of my other working systems.

Is there anything else I can check here before giving up and recompiling shadow without LibPAM?

If you built with systemd it has to be rebuilt after shadow.

No systemd here, just the regular book.

Turns out this was due to the way I was testing it. This is for a headless setup and I was still chrooted. I had to wait until I got openssh / iptables going, boot up natively, and then ssh in as a regular user.

Indeed PAM locks you out if you chroot in as an ordinary user (chroot --userspec ...) and then try to get root. I'm not sure this is a bug or by design, but in any case I jumped the gun and tried to test it out too soon.