Well I finally did manage to update it all. Took me about 9 hours to readd all the things I had added before.
I also found out what the initial problem was, and it had to do with the vB3 Similar Threads hack that I installed. Apparently I had forgotten this step: ALTER TABLE `thread` ADD FULLTEXT(`title`);
I skipped it this time, thinking it was already there, and I had been checking threads out here and there to make sure things were good. Well, I got to this hack, made all the file changes, reloaded a thread and BAM! Got that same error. This time I went back to the beginning of it, ran that query and everything worked wonders.
So basically I could've saved myself 9 hours if I had done that originally, but hey...at least I'm updated now.

Plus it happened while our DNS is still in the process of switching over so I guess it worked out.