This is anything but a normal installation. Normally W98 has to be on the primary on the first IDE bus. If I were you I would 1. install teh hardware as you want to. 2. To verify the hardware at least is working in this configuration, mount the disk from linux. 3. Download Smart Boot Manager from here -
http://fr.rpmfind.net//linux/RPM/sou....7-1.i386.html
There is doc to support it. I have used SMB to boot linux on an older IBM Aptiva that does not support booting from the CD in the Bios. SMB nicley finds all bootable partitions, gives you a list of where you want to boot from. Give that a try. Since I have not tried this myself, I can't be positive it will work, but from what I know I think it may be your best shot.