something else thats worth a go, take a look at your apache error logs from time to time (i often notice people attempting to access none existant files like for example, known buggy web apps) It also may give up some information about people attempting thigns like inserting shell commands into session cookies ?!? (All this results in is the site blocking with a fatel error message)

Here is a question.Is ssh faster at uploading to the server than ftp? I have cable 3meg down 256 up and when uploading files to the server it only uploads at like 30 to 40 kb a sec. .

I find SCP from a windows machine using pscp really slow. scp from a Linux box can use my full bandwidth. Very odd.

Although, btw 256k up is ~32k/s