Hello !
Could you please tell me, what's your VPS configuration ? And type of linux is it ? Do you have any control panel installed that might be eating some resources? I'm thinking about it, 90% ram usage is quite a lot (btw, who did you trace those percents you posted in the project description?), so you probably have a small VPS or some very large databases? Weird enough, since you're saying you only have a couple of small websites running there. However, what needs to be done is analyzing the server, websites, configurations, as a first step, then proceeding to server optimisation, query optimisation and php code optimisation. I am able to start right away and I'll need root access to the server (incl. mysql root, if need be). No upfront payment, everything upon project being successfully completed.
Best regards,
Dragos