I run a web hosting service and have extensive server troubleshooting experience, so I can find out what's going on, what's causing it, and fix it.
I charge per platform/site, so If you have infected sites, I will give you a quote on how much the cleanup would be.
If the server has been rooted (very rare), then the recommendation is to pull the sites off it and move them to a new server.
The plan is to login via SSH and investigate the issue.
PS: If you want to get this done ASAP, let's start now. It's getting late here and tomorrow is my day off.