The site had lots of problems. It's been mostly neglected for the past year or so since I have been busy working on other things. I spent time going through all the error logs and fixed all the issues I found. Mostly, I looked at the performance logs in great detail and was able to see why some of the pages were taking so long to load. The bots didn't help, but they were only part of the problem. Creating new indexes on some of the columns in the database had a huge impact on the speed. With the new indexes, it is able to pull up most of the data for the site from cache instead of having to query the database every time.

With the resources saved from the new indexes and removing the botters, I was also able to start up another instance of the web server to handle twice as much traffic as usual.