The modem port needs to be disabled because the cdrom pretty much sits on the pins. Really the modem pins should be clipped or covered so it doesnt short anything. (I just ripped the connector off the board to cover the pins).
As for the serial pins, they should be in the clear (right now I have my WP in pieces so I cant tell absolutely).
You have to lose the ability to use the built in modem (since it wont fit with the cdrom drive) but a minipci card works great (if you can get the connector or make your own).
I did have to switch to WinME because on a reboot, Win98 doesnt seem to reset the minipci modem/nic properly.