First, I know this is partially due to my own idiocy. When I upgraded from 2.1 to 2.3, one of my WP installations had (I think) the database corrupted in some way and the template tags such as the_content and the_excerpt stopped working. They no longer fetch the content, which is still in the database. I've seen several other cases of this since, all of which seem to happen after something is done to the database, either an upgrade or the installation of something like eFiction.
Instead of scrubbing and re-installing from the backup and trying again, I decided it would be ever so much easier just to write a few direct calls to the database into my theme pages. Yes, I know; please don't say it. I was young and stupid then. Unfortunately, perhaps, this workaround worked and I kept it.
The thing is, after several more upgrades, now at 2.5.1, the template tags still don't work, I have added way too much content to roll back now, and this is starting to cause serious plugin compatibility problems (especially with wordpress-thread-comment, which I would dearly love to use, but which cannot actually post comments with the direct calls to the database worked in).
Is there any way to rebuild my posts table or something? Or anything else anyone can think of to fix this?
Things already attempted (and failed): deactivating all plugins; exporting and reimporting database; complete deletion and re-installation of all php files; exporting post content in xml form and importing it into a fresh installation of both php and tables (failed because there were too many files for the import function to handle).
The site in question: http://www.branchandroot.net/archive/