Well, as usual, after spending much time trying to fix it, I find the answer myself shortly after posting a thread asking for help.
For some reason, CPAN had installed Net::DNS into /home/username/lib instead of /home/username/share, and no matter what I tried, I couldn’t get it to look in both ~/share and ~/lib. So finally, in a moment of duh, I just copied the modules into ~/share (guess I could have linked them, but oh well). Doing that, and setting SA up to use MySQL instead of the filesystem for Bayes, has fixed it up for now. Now I’m getting scores for spam of 37 instead of 0.1.
For all of you who have followed the guide posted in the root post, to get the full potential of SA 3.1.0, you will need to install some CPAN modules into your home directory so it will use the DNS-based tests. If anyone is needs it, I can explain more, but you can figure it out by looking at the logs and using the CPAN shell and man page.