If you don't have the Win98 CD, all may not be lost. Generally the files will still be somewhere on the hard drive, most likely in the locations where the setup program wants to copy them. Now, the way to get around your problem is this: When the setup program asks for the disk, click details, and the details window will show you where the file needs to be copied from (usually from the Win98 CD) and where the file needs to be copied to. If the file already exists on the hard drive, try pointing the browse window at the directory where it wants to copy the file to, in effect making the destination directory (which already contains the file because it was once installed) the source directory. If all goes well Windows will find the source file(s), "copy" it over itself, and go onto the next file(s). Once it's finished and asks for the next set of files, click details, find out where the next file needs to go and make that directory the source in the browse dialog. Repeat ad nauseam until it finishes, reboot or whatever and viola! Everything is back the way it was.
I use this technique constantly at customer's places.
Hope this helps.