You could fire it of with a 3.5" 98 bootdisk and start the computer up with CDROM support and then at the A:> prompt type the following:
sys C: [enter]
wait for the system files transfered message and reboot.
You may also need to fix the MBR. To do this. Start the machine up with the 98 bootdisk and start up with CDROM support and then at the A:> prompt type the following:
fdisk /mbr [enter]
Then reboot with the floppy drive removed from the machine and it should boot from the HDD, and you should be back up and running.
The jumper(s) on your HDD should be set to master. If the CDROM is the slave device on the same cable as the HDD then it needs to set to slave. On some HDD's you may have to set it as master with a slave device, otherwise it won't work properly. If the HDD is on the cable all by itself, then just set it as master and if the CDROM drive is on a cable all by itself then set it to master as well. When you boot up the machine it should detect your drives as follows:
Primary Master (the name of your HDD)
Primary Slave (the name of your CDROM)
Secondary master (none)
Secondary slave (none)
The sbove configuration is how it would appear if both drives were on the same IDE cable.
If they are on different cables then it would appear like this:
Primary Master (the name of your HDD)
Primary slave (none)
Secondary Master (the name of your CDROM)
Secondary slave (none)
About the HDD LED not working. Try reverseing the HDD LED lead that plugs into the motherboard at the front. It is grouped with other plugs like the reset switch, the power LED, the power button, system speaker, etc. You get the picture. Use a flashlight to read the writing on the end of the connectors. This way you will be sure you have the right one. It also may be advisable to revisit your motherboard manual before attempting this. If you don't have one. Do a Google search for it and download it, print it out and read it.
Good Luck.