can you not just add an entry to your grub list for your usb drive?
something like this. assuming your usb drive shows up second.
map (hd0) (hd1)
map (hd1) (hd0)
i believe there are ways to use php4 and php5 in parallel. i'm sure you can find plenty on google about that.
or if you are using apache 2 you can just enable and disable the modules with the following commands as you need. (assuming you have the php4 and php5 packages installed.)
$ a2dismod php4
$ a2enmod php5
$ a2dismod php5
$ a2enmod php4
afterwards restart apache
$ /etc/init.d/apache2 restart