Desktop

It seems, that problem in the boot sequence. Message "Non-system disk or disk error" produced by boot record. So, if you try boot up from "good" floppy startup disk, PC should start. Try switch boot sequence in the BIOS to A,C. If booting from floppy still doesn`t work, try another system floppy. In additin, while bootstrap in progress check that PC boots from floppy.

With best regards,
Vlad.

Go to F10 setup and set all cmos settings to factory default. Let cmos redefine hard disk & other media. This may help.

If setting the CMOS to factory default does not work try this, remove the cmos battery and unplug the power to the motherboard for at least 1 hour. This will completely clear the CMOS out (ATX motherboards still recieve power from the power supply when they are off and just pulling the battery will not work.).

Some alternatives you can try:-

1) Since the system is Win98, why don't you try booting from CD-ROM?

2) Get a new hard disk or any spare hard disk (make sure you have a backup since there is a possibility that your client's harddisk might behit with a virus) which is known to be working with Windows in it, boot up from there. If you can boot from there, then attach your client's hard disk as slave.

3) It may seemed stupid, but did you try to test on other system whether are you able to boot up using your floppy startup disk? No harm trying to create another one and test it again.

Reads like the virus got to the boot.ini and system.ini files and the system is refereing to the system boot disk to recreate the setup files.
you may have to consider going back in and reinstalling the operating system from scratch and running anti-virus to clear up the hard drive.
You can run FDISK and reinstall the operating system and not have to replace the mobo & hdd.Good Luck