Back up critical data.
Assemble boot disk, drivers and manuals.
Boot to Safe Mode.
Open Control Panel/System/Device Manager.
Remove all devices EXCEPT Plug and Play BIOS and Dialup Adaptors.
Shut down and remove all power.
Install new mobo per manual, mount cpu+heatsink, connect floppy, HD, cd-rom and video card.
Power-up with boot floppy. Time to check all switch, LED and device connections. When OK, power down.
Reboot with boot disk and IMMEDIATELY enter BIOS. Set BIOS to BIOS DEFAULTS and configure boot sequence, floppy and HD per mobo manual.
Exit and Save BIOS configuration, shut down and remove boot floppy.
Reboot under win98, let OS detect devices. Install chipset drivers and video adaptor card drivers.
Install other devices one at a time, rebooting after each install.
Final result should be a conflict-free system, with all previous registry tweaks, custom settings and preferences intact. No need to install previous apps, format HD or any other time-consuming BS. This procedure has worked for me several times.