I think you should have left the win98 hdd in there because the bootloader should be installed on the Master Boot Record(MBR)when you dual-boot.If the linux hdd is set as secondary master you should have it read as hdc(x).I'm pretty sure you can set it up the way you describe as long as you leave hda(win98)installed as primary master.
There may be some hacks you can perform to fix this,(without having to reinstall Linux)but that is outside my present scope of knowledge.
When I first tried linux,I went with the dual-boot(Win98/MDK7.1)method,but quickly grew tired of it.Now I have mobile hd trays installed in all my computers and with extra hdd cassettes to hold different OSes.I mostly use Mandrake7.1 for my everyday computing needs,but I have the option to switch to WinNT4 wkstn on one comp and swap WinNT svr or Win2K Pro on another comp.This is because I am taking some Networking courses that use the Windows OSes.Otherwise I would probably have a pure Linux network.
Sorry that I digress.Hope this reply has been of some help
lynch