Maybe this can help you:
I installed Win98 on two different HD's.
Actually, I installed a basic Win98 (with all drivers and other basic progs) on one HD. I "ghosted" this HD with Norton Ghost to another HD. So I had two "identical" HD's.
The HD's are SCSI. One has ID0, the other has ID1.
The beauty of this is, that I can choose from which HD I want to boot. If I disconnect HD 0, the PC automatically boots from HD 1, with the drivers and all the progs properly configured.
Maybe you can do the same with Windows98SE on one HD and the old Win98 on another HD.
I don't know if this is possible with IDE-HD's.