I run a moderately sized forum and I've noticed that some of our threads (which are 300-400pages long) take a longer time to load. It may be affecting the VPS as a whole as well, I was looking through "top -c" and found one MySql process had been running for about 5 hours.
I don't know if it's the huge threads that cause it but sometimes it takes a second or two to just load a page. I've been getting random timeouts as well but they're not so frequent.
mod_evasive isnt going to be affecting your large forum page requests like that. It sounds to me that the software isnt as effecient as it should be. It shouldnt be pulling the data for all the posts in the thread, just counting them to generate a page count. Are you running vbulletin?
I dont think adjusting any of the settings you have listed there are going to help on this specific issue. But a good set for those numbers we often recommend, start with the mysql settings. Pulled from the guide here on wht.
Optimizing your server for efficiency
*** MySQL Optimization***
This will help you to understand how it is possible to optimize MYSQL to fit your needs, hardaware , and mysql current usage.
Here are suggested settings for the my.cnf file. on a server 256mb + ram. You can and should customize these settings specifically for your VPS's usage. . DO NOT change your setting without understanding what it does. Make a backup of your my.cnf before editing the /etc/my.cnf .