OK, pretty much everything in Linux is stored as a plain-text file. Try setting up X as you would normally, but set your mouse/pointer to something like PS2. Then, when you're happy that it all works (apart from the mouse), edit the config file manually and change the appropriate line(s) so that it uses the ttyS0 device.
Alternatively, if you have the option of using /dev/mouse as your input device, try symlinking ttyS0 to mouse prior to running your Xconfig program. For example: (as root) ln -s /dev/ttyS0 /dev/mouse
Hope this helps.