I agree with everyone who said that your problems most likely have something to do with having hardware that Windows 98 SE doesn't know how to drive.
I don't know anyone who has attempted this, or even really thought of attempting this, but if you are a masochist with too much time on his hands who is really intent on running Windows 98 SE, you could try replacing the underlying DOS (7.0, I think) with FreeDOS
. Since the old Windows 9x versions, including Windows 98 SE, are essentially Windows on top of DOS, even though they shipped with DOS integrated already, it may be possible. The main advantage, if you can get this to work, is that FreeDOS is open-source and supports much more modern hardware than Windows 98 SE. I see no reason why it wouldn't - if you can manage to integrate it properly - since FreeDOS is 100% binary compatible with MS-DOS. I admit that I am not overly familiar with DOS architecture and may be overlooking some aspect of Windows 98 SE or FreeDOS design that would prevent this, but it might be worth a try!
If you're not married to Windows 98 SE, however, it might be interesting to try ReactOS
instead. While its still in alpha and not likely to be complete for quite some time, it generally supports older hardware quite nicely. It might run decently on your machine, and it would certainly be a lot easier to install and run modern software on if