1. you cannot install fonts in windows by copying files into the font directory.
2. You can cause windows to crash by removing font files without uninstalling the font first.
As to autoexec and config; unless you need to have dos mode drivers installed, you are better off having both of these files as empty blank files.
The only exception is some programs such as Anti-virus and boot managers that run before the OS is loaded.
Cleanup autexec and config as best you can. Save the originals in case you do need a specific line of code.
Boot from the floppy, and re-install 98.
This should take care of any required fonts that are missing.
If enough damage has been done, you may need to delete the registry files and re-install windows.
The negative of this is that you will need to re-install all of your applications, and reset your GUI settings.
One extra benefit, is that you will have a cleaner system.
You will need to run a registry cleaner to clean up the remnants of the missing fonts. I use Norton WinDoctor, and Meijenix Fix-It.
Reducing the number of fonts is a good way to speed up windows.
Remove fonts from the font icon in control panel.