The memory, as installed, should be OK, those 440 boards weren't usually too fussy.
Win 98 should have the appropriate drivers for the disk controllers, but check in the control panel to see if perhaps they are running in 'real mode' . Updating the drivers from a Win98 disk ought to do the trick. Or, Computer Technician number 1,2,3 etc., tried, through software, to enable something higher than UDMA 33. Those motherboards won't do any faster and trying to make them do so just fouls them up.
Finally, in the Control Panel, take a look to see if the hard drive has DMA enabled. This can make a HUGE difference in HDD speed and throughput. The WD is certainly DMA capable, so if you get a warning, you can safely ignore it.
The boot-up time issue really does point to hard drive speed.