This is an update post since we have now completely redone the article section. The issues we were having that were described in the quote above were unfortunately still happening. It had to be a database issue, but I could never find it.
Because of this, I wanted to move to a new article section. The only issue with that was having to rebuild the entire article section. There are well over 200 articles and just thinking about that was daunting. However I did start it, but quickly realized if I worked hard on the article section, it would just fill the forum up with articles. For this reason, I started only doing a couple a day. Then, it clicked....
Why not just purchase the new AMS that is made for this new version of the forum software.... Yes, it costs money, true, it may not work, but IMO, it was worth a shot.
To my surprise, it seems that the new system has overwritten the database tables and resolved the issues that I was seeing on the old forum. So the new Article section is as fast as the rest of the website, and has all of the information behind the same links as before. So no need to do any rewrite rules to correct broken links. I am very happy about not having to do weeks worth of work.
Please let me know what you think about the new article section. As always, I'm taking suggestions for improvements.