If the files were uploaded in binary mode could cause this error. Please try uploading the files in ASCII mode. If that doesn't solve it, please open a ticket with the help desk. They can help you sort out a 500 error.
You can't with the cPanel version of phpAdmin. Not sure you can install a version in your own web space that they would be able to use but something to look into.
The server should accept a url with a ? in it. If it didn't how would you pass variables? Maybe it has something to do with you defiing the folder as a subdomain. You can open a ticket with the help desk. Maybe they can point you in the right direction.
How did you create the subdomain? How are you trying to access it?
>http://subdomain.mydomain.ext
Did you run the installer for WP in the wp-admin folder?
I've been updating all along so I am not sure you if you would have problems but I would assume not. Just be sure to have backups in case something goes wrong.
I would backup the the database and the whole wordpress folder you installed into. Select the HOME backup function and then backup the database through the cPanel backup functions.
You need to change the mail command to this
>mail($to, $subject, $message, $headers, '-fwebmaster@example.com')
Change webmaster@example.com to what ever email address you want it to be from.