Nathan,
Before you attempt to repair Windows, let's try and find the root cause of your problem.
How much system RAM do you have?
How old is this installation of W98?
How much free hard drive space do you have?
How large are the registry files, user.dat, system.dat, ?
What if any system utilities do you run?
What video card do you have?
Which version of Internet Explorer and DirectX are installed?
Please reject my answer, and add a comment with the answers to the questions.
Realistically, with the problems you have, a fresh clean installation of W98 is the "BEST" way to fix your problems.
You can do this WITHOUT formatting your hard drive.
You will however need to reinstall your application software.
Start by downloading and saving the latest drivers for ALL hardware.
Next, boot from a W98 startup disk.
Browse to C:\Windows
Then, start deleting files.
Use the DOS delete *.* command.
(Note: you will loose any 3rd party screen savers that are installed.)
Enter the sub-folders \Temp and \System
Delete all files and files in sub-folders here also.
Switch to the "root" folder C:\
Check the folder for any personal files using the dir command.
Delete all files except your personal files.
Insert your Windows CD.
From the A: prompt, run setup.
Chas