Before you make the switch, go into the registry in Win98. (run regedit.exe) Go to HKEY_LOCAL_MACHINE\Enum.
Delete the Enum key. Close regedit.exe. Shutdown windows immediately before it starts detecting hardware again. Install the new motherboard. Bootup. It will redetect ALL your hardware, including your new motherboard settings.
Note: Have all your drivers for hardware ready to install (as in updated drivers that didn't originally come with Win98, like your videocard, modem's or zip drive, or any hardware peripheral).
Also, have your new motherboard's drivers handy, if need be.