Goob, I'm not sure what you have figured out at this point... but I manage a few servers and I can give some suggestions.
First of all, make sure the vBulletin software is up to date. They're constantly tweaking things and making sure it's running as fast as it can be.
Also, in the Admin CP, there are tools at the bottom of the navigation. Repair/optimize and select all the tables in the database and run the tool on them. This will clear up the overhead, and make sure the database is working as efficiently as possible.
I would also run the misc. tools, like removing anything labeled as "orphan" to clean things up a little bit.