Do not think that this is anything to do with the hard drive. More likely to be System resources - see here for brief explanation
Not sure how to make a blue link!
To check the level or resources you can activate the resource meter through Start/programs/accessories/system tools
This places the reource meter in the system tray. If the meter is not there then it can be quickly installed from the W98 Cd through control Panel/ add software/windows setup/system tools select details then select resource meter and ok to install.
To get a better idea of the exact level of resources in use, right click on the resource meter icon and choose Details from the menu. This will be displayed in %. The lower they get the more likely you are to have problems - say below 40%.
If you start the meter up when you first start the pc you will be able to see the level at which you start off. If this is already low then you may have too many start up items. I have an older PC with W98 and a bare minimum of start up items and it starts with all resources at 95%.
Some programs hog resources and do not release them when shut down. There are progs available to sort out this sort of problem but off hand cannot remember names.
Hope this is of some help.