“Easy” Reinstalling of Windows 98

Following a tech-site’s posted “tip”, I reinstalled Win 98 after first changing the name of “WIN.COM” (this was done to save my old icons and settings) and making “SYSTEM.DAT” accessible in case I needed to undo the new install. When I reinstalled Win 98, the old programs and icons were saved allright, but now all the file associations (mostly DLL files) are “missing” and the programs are inaccessable. Windows placed the new install in a “Windows001” folder. I tried changing the Registry settings to point to the old “Windows” folder–didn’t work. How can I re-associate the old programs with the missing files?