Since explorer is shut down before I can actually access the desktop, it is impossible for me to try fixing this from within the OS, so any solutions that require the os to be running are unusable.
Pressing ok to dismiss the alert then causes explorer to say it performed an illegal operation and will be shut down. The installation process runs fine without any problems, but then when it tries to load the desktop for the first time it pops up with an error message saying 'the SHEL元2.DLL file is linked to missing export SHLWAPI.DLL:tFileAttributesA.'.
This is concerning the Windows 98 SE OEM (full) iso listed near the top of the windows 98 releases page on this site.
