After many many many months of struggling and frustration, I finally figured out what was wrong with Tomorrowlands' scripts. The upshot: The journal script works! Journal permalinks work! About freakin' time!
It'll take some more rebuilding to get the adult-files script, the contact script, the comics-display script, et.al. working again, but at least the major block has been removed.
Edited to add: I cannot emphasize enough what an incredible feeling it is to have this change made. The practical effect is tiny, but my website feels fixed, dammit. This has been hanging over my head pretty much continuously since the server crash in 2005.