Server updated.
The new McRegion-ified world shrunk from 126 to 110 MB, and so far the timing error that coincided with the regular sun/moon skipping seems to be greatly reduced. Of course, that could be in part because I'm the only on the server now.
Also, I've enabled the built-in whitelist and imported all of the users I had as non-guest members with SimpleServer. If you want in and you're not on the list, just let me know!
Remember to switch back to the default Minecraft texture pack until I get an update ready. Otherwise, all new blocks will be invisible or otherwise busted.