You could track down every missing .exe file, but a reinstall would be much easier. Win98 installer refuses to run from DOS mode if it finds a Windows installation. If you run the Windows 98 installer in Windows, however, it will automatically detect your Win98 directory and reinstall the files, keeping your original settings, color shemes, installed apps, etc. If you do this, Win98 should function normally.
--Good luck from Mr. Nobody