I haven't had time to read a lot of of that, but I caught the zombie processes bit, and I agree, that is a problem. On one of my dedicated threads servers, I can have about 300 processes, server loads under 1, and 0 zombie processes.
So IMO, you have way too many zombie processes for one. I don't know if that is ultimately your problem, but a properly setup server and/or software should not lead to that many zombie (defunct) processes.
I'll try to take a look at all the numbers and stats you posted earlier.. but in the meantime, can you say what OS you are using, kernel version, etc?