I decided to reinstall win98SE, and attached both HDD and DVD-ROM to the secondary IDE channel. It succeeded, but the screen did go black at the very end of the installation. I solved that by using the UIDE for the HDD from that point onwards.

I've got a question - say if both IDE ports are defective, is it possible to add in a PCI based card which is completely ATAPI compatible for the DVD-ROM drive? I understand that Raid cards don't do ATAPI very well. What I need is some kind of 100% IDE replacement, because I know for certain now that IDE 1 is defective, and I'm not 100% convinced that IDE 2 is working completely correctly.