Please don't ask details about how I've ended up to where I'm at now. I've got no time to explain.
I did a Win98se install from a genuine MS CD-ROM onto a system that had been upgraded from Win95 to Win98 with an upgrade disk. Instead of installing into the existing C:\Windows folder, I chose the given directory of C:\Windows.000 to copy my files into during the installation.
Now that I've completed the install, I've discovered that my links in my start menu are missing. No problem, I'll just copy the shortcuts over from my original C:\windows\start menu directory. Anyway, although the links are there, anytime that I select a program to open up, I'm told that there are missing DLLs and other files. Some programs ask me to reinstall the program. I really don't want to go through all that.
I'm wondering if I do a second Win98se reinstall, and select the C:\windows directory to install into. Would that fix my problems?