If you've tried the 'repair' option, you'll have to reinstall 98 to fix ie:
To install IE 5.5/or 6, you must first reinstall the default IE 5.0 by reinstalling Windows. To do this, you must have either the Windows 98 SE CD, or a copy of the installation (CAB) files on the hard disk.
To determine if the CAB files are on the hard disk, click Start, point to Find, and click Files and Folders. From the "Look in" dropdown menu, choose Local hard drives. In "Named", enter Win98*.CAB, then click Find Now. The correct folder will contain dozens of matching files. Note the path to the folder.
To install IE 5.0 during Windows installation, locate the file C:\Windows\System\IEMIGRAT.DLL (you can use Find). Right-click the IEMIGRAT.DLL file, then click Rename and change the filename to IEMIGRAT.OLD.
Disable your antivirus, and reinstall Windows by running Setup.exe on the Windows CD; or Setup.exe in the CAB files folder on the hard disk.
After the reinstallation (30 to 45 minutes), install IE 5.5 or 6; then obtain the latest security patches from Windows Update.