I finished setting up the new Linux box last night. It hasn't been physically moved into place: I'll do that tonight. But all the software is installed and working.
Now that the security problem is resolved, transferring over MySQL seemed very easy using mysqldump but I'm far from certain that it actually worked: very little was dumped, and when I tried to look at MySQL on the old system I see no databases. That was set up for me by someone else, so I don't know what's supposed to be there, but it seems like it was supposed to be more than that. I'm waiting to hear back from the person who set it up.
Transferring over CVS took a bit more doing since I didn't have the original directions by which I'd set it up. I had copied over the directories that I was CVSing but I wasn't able to get a connection without a password, and all my guesses about the password were wrong. Finally I found I did have the directions, and following them, I was able to get it not only working, but better than before. It used to always prompt me for my PGP passphrase, but now it doesn't. What a convenience that'll be.
To save myself reconfiguring a lot of things, I swapped IP addresses now so the new server (Torus) is on the same IP that the old server (Papyrus) was on. Right now they're both powered up, Papyrus still in the basement, Torus still upstairs. Tonight, after I do a DVD backup of Torus, I'll power down Papyrus (but keep it set up for a bit longer in case I need to recover anything from it), and move Torus down to where Papyrus was. (Poor Torus has had a nice roomy flatscreen monitor and is going to moved to an ancient CRT monitor when it gets moved, since the flatscreen is borrowed, but since I rarely access it directly, it doesn't really matter.)
Boy, does it compile, load, CVS, and shut down a lot faster than the old Pentium II it replaced. How luxurious.