I just upgraded the site to WordPress 2.1. Please bear with the site as I make sure all the customizations work. (Yeah, I know, living dangerously by not waiting a few days.)
Right now the category tabs are showing all categories instead of just the top three… but only on single posts.
OK. That’s fixed. Apparently WP 2.1 removed the ability to list only the top-level categories, and caching was half-enabled. I also had to apply the fix for PHP 5.2 again. (I really figured they would have fixed that by now!)
Everything else seems to still work, except for the word stats plugin and wp-amazon plugin. Both are composing plugins, and I wasn’t really using either of them anymore.
Update Jan. 25: I also updated WP-Cache to version 2.0.22, and it doesn’t work quite right. In particular, it won’t clear the cached copy of a page after someone posts a comment. I’ve reverted the cache to 2.0.17+tweaks for now, which seems to work.