|"Invalid system disk" means you're trying to boot from a drive with no system files. |
After booting from the bootdisk type dir/p c:\. See if it shows a WINDOWS directory. If not you have no choice but to reinstall.
If it does show a windows directory then maybe you can get by by just refreshing the system files. After booting from the bootdisk type sys c: and enter. That should make the C: drive bootable but it may not go into windows. If it just stops at the c:\> prompt then you'll need to overwrite the dos version of msdos.sys with the windows version.
But first post back results of the above. Also post back the version of 98 you have--first or second edition. If you don't know, when doing the dir/p c:\, look for a COMMAND.COM file and post back its date.