On the certs.. You have more than one IP number right? You can only use one cert per IP number.
The logs look like what most of us running serves see fairly regularly. These probes come and go kinda in waves from my experience (Been running my own webservers since 2000)
As to your specific problem with 500 errors, If these errors occur while valid users attempting to access their websites then I'm not sure where to point you...if they are just random 500 errors showing up in your log files then that may be a result of these probers trying to "form feed" an existing script on your server with data that causes the script to barf. That would be a good thing actually as it shows that their attempts are futile.
Just my input.. hope it helps.